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cd $HOME/workshop/2024-2/session6_smallRNAseq/runs/run2_human_MirGeneDB

cp $HOME/workshop/2024-2/session6_smallRNAseq/data/human_disease/samplesheet.csv .
cp $HOME/workshop/2024-2/session6_smallRNAseq/scripts/nextflow.config .
cp $HOME/workshop/2024-2/session6_smallRNAseq/scripts/launch_nf-core_smallRNAseq_MirGeneDB.pbs .

cat launch_nf-core_smallRNAseq_MirGeneDB.pbs

qsub launch_nf-core_smallRNAseq_MirGeneDB.pbs

qjobs

results/
├── bowtie_index
│   ├── mirna_hairpin
│   └── mirna_mature
├── fastp
│   └── on_raw
├── fastqc
│   ├── raw
│   └── trimmed
├── mirna_quant
│   ├── bam
│   ├── edger_qc <-- Expression mature miRNA (mature_counts.csv) and precursor-miRNAs (haripin_counts.csv)
│   ├── mirtop
│   ├── reference
│   └── seqcluster
├── mirtrace
│   ├── mirtrace-report.html
│   ├── mirtrace-results.json
│   ├── mirtrace-stats-contamination_basic.tsv
│   ├── mirtrace-stats-contamination_detailed.tsv
│   ├── mirtrace-stats-length.tsv
│   ├── mirtrace-stats-mirna-complexity.tsv
│   ├── mirtrace-stats-phred.tsv
│   ├── mirtrace-stats-qcstatus.tsv
│   ├── mirtrace-stats-rnatype.tsv
│   ├── qc_passed_reads.all.collapsed
│   └── qc_passed_reads.rnatype_unknown.collapsed
├── multiqc
│   ├── multiqc_data
│   ├── multiqc_plots
│   └── multiqc_report.html
└── pipeline_info
    ├── execution_report_2024-08-26_14-38-10.html
    ├── execution_report_2024-08-26_17-44-50.html
    ├── execution_timeline_2024-08-26_14-38-10.html
    ├── execution_timeline_2024-08-26_17-44-50.html
    ├── execution_trace_2024-08-26_17-44-50.txt
    ├── nf_core_smrnaseq_software_mqc_versions.yml
    ├── params_2024-08-26_17-45-00.json
    ├── pipeline_dag_2024-08-26_14-38-10.html
    └── pipeline_dag_2024-08-26_17-44-50.html

cd /results/mirna_quant/edger_qc

├── hairpin_counts.csv
├── hairpin_CPM_heatmap.pdf
├── hairpin_edgeR_MDS_distance_matrix.txt
├── hairpin_edgeR_MDS_plot_coordinates.txt
├── hairpin_edgeR_MDS_plot.pdf
├── hairpin_log2CPM_sample_distances_dendrogram.pdf
├── hairpin_log2CPM_sample_distances_heatmap.pdf
├── hairpin_log2CPM_sample_distances.txt
├── hairpin_logtpm.csv
├── hairpin_logtpm.txt
├── hairpin_normalized_CPM.txt
├── hairpin_unmapped_read_counts.txt
├── mature_counts.csv  <-- Expression profile of mature miRNAs.
├── mature_CPM_heatmap.pdf
├── mature_edgeR_MDS_distance_matrix.txt
├── mature_edgeR_MDS_plot_coordinates.txt
├── mature_edgeR_MDS_plot.pdf
├── mature_log2CPM_sample_distances_dendrogram.pdf
├── mature_log2CPM_sample_distances_heatmap.pdf
├── mature_log2CPM_sample_distances.txt
├── mature_logtpm.csv
├── mature_logtpm.txt
├── mature_normalized_CPM.txt
└── mature_unmapped_read_counts.txt

cat mature_counts.csv

"","Hsa-Let-7-P1b_5p","Hsa-Let-7-P1c_5p","Hsa-Let-7-P1d_5p","Hsa-Let-7-P2a1_5p","Hsa-Let-7-P2a2_5p","Hsa-Let-7-P2a3_5p","Hsa-Let-7-P2b1_5p","Hsa-Let-7-P2b2_5p","Hsa-Let-7-P2b3_5p","Hsa-Let-7-P2c1_5p","Hsa-Let-7-P2c2_5p","Hsa-Let-7-P2c3_5p","Hsa-Mir-1-P1_3p","Hsa-Mir-1-P2_3p","Hsa-Mir-1-P3_3p","Hsa-Mir-7-P1_5p","Hsa-Mir-7-P2_5p","Hsa-Mir-7-P4_5p","Hsa-Mir-8-P1a_3p","Hsa-Mir-8-P1b_3p","Hsa-Mir-8-P2a_3p","Hsa-Mir-8-P2b_3p","Hsa-Mir-8-P3a_3p","Hsa-Mir-9-P1_5p","Hsa-Mir-9-P1_3p","Hsa-Mir-9-P2_5p","Hsa-Mir-9-P2_3p","Hsa-Mir-9-P3_5p","Hsa-Mir-9-P3_3p","Hsa-Mir-10-P1b-v1_5p","Hsa-Mir-10-P1b-v2_5p","Hsa-Mir-10-P1c-v1_5p","Hsa-Mir-10-P1c-v2_5p","Hsa-Mir-10-P2b_5p","Hsa-Mir-10-P2c_5p","Hsa-Mir-10-P2d_5p","Hsa-Mir-10-P3b_5p","Hsa-Mir-10-P3c_5p","Hsa-Mir-10-P3d_5p","Hsa-Mir-15-P1a_5p","Hsa-Mir-15-P1b_5p","Hsa-Mir-15-P1c_5p","Hsa-Mir-15-P1d_5p","Hsa-Mir-15-P2a_5p","Hsa-Mir-15-P2b_5p","Hsa-Mir-15-P2c_5p","Hsa-Mir-15-P2d_5p","Hsa-Mir-17-P1a_5p","Hsa-Mir-17-P1c_5p","Hsa-Mir-17-P1d_5p","Hsa-Mir-17-P1d_3p","Hsa-Mir-17-P2a_5p","Hsa-Mir-17-P2c_5p","Hsa-Mir-17-P4a_5p","Hsa-Mir-17-P4c_5p","Hsa-Mir-17-P4d_5p","Hsa-Mir-19-P1a_3p","Hsa-Mir-19-P2a_3p","Hsa-Mir-19-P2c_3p","Hsa-Mir-21_5p","Hsa-Mir-22-P1b_3p","Hsa-Mir-23-P2_3p","Hsa-Mir-23-P3_3p","Hsa-Mir-24-P2_3p","Hsa-Mir-24-P3_3p","Hsa-Mir-26-P1_5p","Hsa-Mir-26-P2_5p","Hsa-Mir-26-P4_5p","Hsa-Mir-27-P2_3p","Hsa-Mir-27-P3_3p","Hsa-Mir-28-P1_5p","Hsa-Mir-28-P1_3p","Hsa-Mir-28-P2_5p","Hsa-Mir-28-P2_3p","Hsa-Mir-28-P3_5p","Hsa-Mir-29-P1b-v1_3p","Hsa-Mir-29-P1b-v2_3p","Hsa-Mir-29-P1d-v1_3p","Hsa-Mir-29-P1d-v2_3p","Hsa-Mir-29-P2b_3p","Hsa-Mir-29-P2d_3p","Hsa-Mir-30-P1a_5p","Hsa-Mir-30-P1b_5p","Hsa-Mir-30-P1d_5p","Hsa-Mir-30-P2a_5p","Hsa-Mir-30-P2b_5p","Hsa-Mir-30-P2d_5p","Hsa-Mir-31_5p","Hsa-Mir-32_5p","Hsa-Mir-33-P1_5p","Hsa-Mir-33-P3_5p","Hsa-Mir-34-P1_5p","Hsa-Mir-34-P2a_5p","Hsa-Mir-34-P2a_3p","Hsa-Mir-34-P2b_5p","Hsa-Mir-34-P3a-v1_5p","Hsa-Mir-34-P3a-v2_5p","Hsa-Mir-34-P3b_5p","Hsa-Mir-34-P3b_3p","Hsa-Mir-34-P3c_5p","Hsa-Mir-92-P1a_3p","Hsa-Mir-92-P1c_3p","Hsa-Mir-92-P1d_3p","Hsa-Mir-92-P2a_3p","Hsa-Mir-92-P2c_3p","Hsa-Mir-92-P2d_3p","Hsa-Mir-95-P1_3p","Hsa-Mir-95-P2_3p","Hsa-Mir-95-P3-v1_5p","Hsa-Mir-95-P3-v2_5p","Hsa-Mir-95-P4_5p","Hsa-Mir-95-P4_3p","Hsa-Mir-96-P1_5p","Hsa-Mir-96-P2_5p","Hsa-Mir-96-P3-v1_5p","Hsa-Mir-96-P3-v2_5p","Hsa-Mir-101-P1-v1_3p","Hsa-Mir-101-P1-v2_3p","Hsa-Mir-101-P2-v1_3p","Hsa-Mir-101-P2-v2_3p","Hsa-Mir-103-P1_3p","Hsa-Mir-103-P2_3p","Hsa-Mir-103-P4_3p","Hsa-Mir-105-P1_5p","Hsa-Mir-105-P2_5p","Hsa-Mir-122_5p","Hsa-Mir-124-P1-v1_3p","Hsa-Mir-124-P1-v2_3p","Hsa-Mir-124-P2-v1_3p","Hsa-Mir-124-P2-v2_3p","Hsa-Mir-124-P3-v1_3p","Hsa-Mir-124-P3-v2_3p","Hsa-Mir-126-P2-v1_3p","Hsa-Mir-126-P2-v2_5p","Hsa-Mir-126-P2-v3_3p","Hsa-Mir-127_3p","Hsa-Mir-128-P1_3p","Hsa-Mir-128-P2_3p","Hsa-Mir-129-P1_3p","Hsa-Mir-129-P2_5p","Hsa-Mir-129-P2_3p","Hsa-Mir-130-P1c_3p","Hsa-Mir-130-P2a_3p","Hsa-Mir-130-P2b_3p","Hsa-Mir-130-P3b_3p","Hsa-Mir-130-P4a_5p","Hsa-Mir-130-P4a_3p","Hsa-Mir-132-P1_3p","Hsa-Mir-132-P2_5p","Hsa-Mir-132-P2_3p","Hsa-Mir-133-P1-v1_3p","Hsa-Mir-133-P1-v2_3p","Hsa-Mir-133-P2-v1_3p","Hsa-Mir-133-P2-v2_3p","Hsa-Mir-133-P3-v1_3p","Hsa-Mir-133-P3-v2_3p","Hsa-Mir-134_5p","Hsa-Mir-135-P1_5p","Hsa-Mir-135-P2_5p","Hsa-Mir-135-P4_5p","Hsa-Mir-136-v1_3p","Hsa-Mir-136-v2_5p","Hsa-Mir-136-v2_3p","Hsa-Mir-137-P1-v1_3p","Hsa-Mir-137-P1-v2_3p","Hsa-Mir-138-P1_5p","Hsa-Mir-138-P2_5p","Hsa-Mir-139_5p","Hsa-Mir-140-P1-v1_3p","Hsa-Mir-140-P1-v2_3p","Hsa-Mir-142-P1-v1_5p","Hsa-Mir-142-P1-v2_3p","Hsa-Mir-142-P1-v3_3p","Hsa-Mir-142-P1-v4_5p","Hsa-Mir-143_3p","Hsa-Mir-144-v1_3p","Hsa-Mir-144-v2_3p","Hsa-Mir-145_5p","Hsa-Mir-146-P1_5p","Hsa-Mir-146-P4_5p","Hsa-Mir-147-v1_3p","Hsa-Mir-147-v2_3p","Hsa-Mir-148-P1_3p","Hsa-Mir-148-P3_3p","Hsa-Mir-148-P4_3p","Hsa-Mir-149_5p","Hsa-Mir-150_5p","Hsa-Mir-153-P1_3p","Hsa-Mir-153-P2_3p","Hsa-Mir-154-P1_5p","Hsa-Mir-154-P1_3p","Hsa-Mir-154-P2-v1_5p","Hsa-Mir-154-P2-v2_5p","Hsa-Mir-154-P3a-v1_3p","Hsa-Mir-154-P3a-v2_3p","Hsa-Mir-154-P3b_3p","Hsa-Mir-154-P4a_3p","Hsa-Mir-154-P4b_3p","Hsa-Mir-154-P5_5p","Hsa-Mir-154-P5_3p","Hsa-Mir-154-P6_3p","Hsa-Mir-154-P7_5p","Hsa-Mir-154-P8_5p","Hsa-Mir-154-P8_3p","Hsa-Mir-154-P9_3p","Hsa-Mir-154-P10_5p","Hsa-Mir-154-P12_3p","Hsa-Mir-154-P13-v1_5p","Hsa-Mir-154-P13-v2_5p","Hsa-Mir-154-P14_5p","Hsa-Mir-154-P15_5p","Hsa-Mir-154-P16_3p","Hsa-Mir-154-P17_3p","Hsa-Mir-154-P18_3p","Hsa-Mir-154-P19_3p","Hsa-Mir-154-P20-v1_3p","Hsa-Mir-154-P20-v2_3p","Hsa-Mir-154-P21_3p","Hsa-Mir-154-P22_3p","Hsa-Mir-154-P23_3p","Hsa-Mir-154-P24_3p","Hsa-Mir-154-P25_3p","Hsa-Mir-154-P26_3p","Hsa-Mir-154-P27_3p","Hsa-Mir-154-P28a_3p","Hsa-Mir-154-P28b_5p","Hsa-Mir-154-P28b_3p","Hsa-Mir-154-P29_3p","Hsa-Mir-154-P30_3p","Hsa-Mir-154-P36_3p","Hsa-Mir-155_5p","Hsa-Mir-181-P1a_5p","Hsa-Mir-181-P1b_5p","Hsa-Mir-181-P1c_5p","Hsa-Mir-181-P2a_5p","Hsa-Mir-181-P2b_5p","Hsa-Mir-181-P2c_5p","Hsa-Mir-184_3p","Hsa-Mir-185_5p","Hsa-Mir-186_5p","Hsa-Mir-187_3p","Hsa-Mir-188-P1_5p","Hsa-Mir-188-P2_5p","Hsa-Mir-188-P3_5p","Hsa-Mir-190-P1_5p","Hsa-Mir-190-P3_5p","Hsa-Mir-191_5p","Hsa-Mir-192-P1_5p","Hsa-Mir-192-P2_5p","Hsa-Mir-193-P1a_3p","Hsa-Mir-193-P1b_5p","Hsa-Mir-193-P2a_3p","Hsa-Mir-193-P2b_3p","Hsa-Mir-194-P1_5p","Hsa-Mir-194-P2_5p","Hsa-Mir-196-P1_5p","Hsa-Mir-196-P3_5p","Hsa-Mir-196-P4_5p","Hsa-Mir-197_3p","Hsa-Mir-199-P1-v1_3p","Hsa-Mir-199-P1-v2_3p","Hsa-Mir-199-P1-v3_3p","Hsa-Mir-199-P2-v1_3p","Hsa-Mir-199-P2-v2_3p","Hsa-Mir-199-P2-v3_3p","Hsa-Mir-199-P3-v1_3p","Hsa-Mir-199-P3-v2_3p","Hsa-Mir-199-P3-v3_3p","Hsa-Mir-202_5p","Hsa-Mir-203-v1_3p","Hsa-Mir-203-v2_3p","Hsa-Mir-204-P1_5p","Hsa-Mir-204-P2_5p","Hsa-Mir-205-P4_5p","Hsa-Mir-208-P1_3p","Hsa-Mir-208-P2_3p","Hsa-Mir-210_3p","Hsa-Mir-214-v1_3p","Hsa-Mir-214-v2_3p","Hsa-Mir-216-P2a_5p","Hsa-Mir-216-P2b_5p","Hsa-Mir-217-v1_5p","Hsa-Mir-217-v2_5p","Hsa-Mir-218-P2_5p","Hsa-Mir-218-P4_5p","Hsa-Mir-219-P2_5p","Hsa-Mir-219-P2_3p","Hsa-Mir-219-P2-as_5p","Hsa-Mir-219-P2-as_3p","Hsa-Mir-219-P3_3p","Hsa-Mir-221-P1a_3p","Hsa-Mir-221-P2a_5p","Hsa-Mir-221-P2a_3p","Hsa-Mir-223_3p","Hsa-Mir-224_5p","Hsa-Mir-296_5p","Hsa-Mir-320-P1_3p","Hsa-Mir-320-P2a_3p","Hsa-Mir-320-P2b_3p","Hsa-Mir-320-P3_3p","Hsa-Mir-320-P4_3p","Hsa-Mir-324_5p","Hsa-Mir-325_3p","Hsa-Mir-326_3p","Hsa-Mir-328_3p","Hsa-Mir-330-v1_3p","Hsa-Mir-330-v2_3p","Hsa-Mir-331_3p","Hsa-Mir-335_5p","Hsa-Mir-335_3p","Hsa-Mir-337-as_5p","Hsa-Mir-337-as_3p","Hsa-Mir-337-v1_5p","Hsa-Mir-337-v1_3p","Hsa-Mir-337-v2_5p","Hsa-Mir-337-v2_3p","Hsa-Mir-338-P2_3p","Hsa-Mir-338-P2-as_5p","Hsa-Mir-338-P2-as_3p","Hsa-Mir-339_5p","Hsa-Mir-339_3p","Hsa-Mir-340_5p","Hsa-Mir-342_3p","Hsa-Mir-345_5p","Hsa-Mir-346_5p","Hsa-Mir-361-v1_5p","Hsa-Mir-361-v2_3p","Hsa-Mir-362-P1_5p","Hsa-Mir-362-P2-v1_3p","Hsa-Mir-362-P2-v2_3p","Hsa-Mir-362-P3_3p","Hsa-Mir-362-P4_3p","Hsa-Mir-362-P5_5p","Hsa-Mir-370_3p","Hsa-Mir-374-P1_5p","Hsa-Mir-374-P1_3p","Hsa-Mir-374-P2_5p","Hsa-Mir-375_3p","Hsa-Mir-376-P1_3p","Hsa-Mir-376-P2_3p","Hsa-Mir-376-P3_3p","Hsa-Mir-376-P4_3p","Hsa-Mir-376-P5_3p","Hsa-Mir-378_3p","Hsa-Mir-383-v1_5p","Hsa-Mir-383-v2_5p","Hsa-Mir-423_5p","Hsa-Mir-423_3p","Hsa-Mir-425_5p","Hsa-Mir-430-P1_3p","Hsa-Mir-430-P2_3p","Hsa-Mir-430-P3_3p","Hsa-Mir-430-P4_3p","Hsa-Mir-430-P5_5p","Hsa-Mir-430-P5_3p","Hsa-Mir-430-P6_3p","Hsa-Mir-430-P7_3p","Hsa-Mir-430-P8a_3p","Hsa-Mir-430-P8b_3p","Hsa-Mir-430-P9a_5p","Hsa-Mir-430-P9a_3p","Hsa-Mir-430-P9b_5p","Hsa-Mir-430-P9b_3p","Hsa-Mir-430-P10_3p","Hsa-Mir-430-P11_3p","Hsa-Mir-430-P12_5p","Hsa-Mir-430-P13_5p","Hsa-Mir-430-P14_3p","Hsa-Mir-430-P15_5p","Hsa-Mir-430-P16_3p","Hsa-Mir-430-P17_5p","Hsa-Mir-430-P18_5p","Hsa-Mir-430-P18_3p","Hsa-Mir-430-P19_3p","Hsa-Mir-430-P21_3p","Hsa-Mir-430-P22_3p","Hsa-Mir-430-P23_3p","Hsa-Mir-430-P24_3p","Hsa-Mir-430-P25_3p","Hsa-Mir-430-P26_3p","Hsa-Mir-430-P27a_3p","Hsa-Mir-430-P27b_3p","Hsa-Mir-430-P29a_3p","Hsa-Mir-430-P29b_3p","Hsa-Mir-430-P31a_5p","Hsa-Mir-430-P31b_5p","Hsa-Mir-430-P33_5p","Hsa-Mir-430-P34_5p","Hsa-Mir-430-P35a_3p","Hsa-Mir-430-P35b_3p","Hsa-Mir-430-P35c_3p","Hsa-Mir-430-P38_3p","Hsa-Mir-430-P39_3p","Hsa-Mir-430-P41_3p","Hsa-Mir-430-P42_3p","Hsa-Mir-430-P43_5p","Hsa-Mir-430-P43_3p","Hsa-Mir-430-P44_5p","Hsa-Mir-430-P45_5p","Hsa-Mir-430-P46_5p","Hsa-Mir-430-P47_5p","Hsa-Mir-430-P48_5p","Hsa-Mir-430-P49_5p","Hsa-Mir-430-P50_5p","Hsa-Mir-431_5p","Hsa-Mir-431_3p","Hsa-Mir-432_5p","Hsa-Mir-433_3p","Hsa-Mir-448_5p","Hsa-Mir-448_3p","Hsa-Mir-450-P1_5p","Hsa-Mir-450-P2_5p","Hsa-Mir-450-P3_5p","Hsa-Mir-451_5p","Hsa-Mir-452-v1_5p","Hsa-Mir-452-v2_5p","Hsa-Mir-455_5p","Hsa-Mir-459_5p","Hsa-Mir-483_5p","Hsa-Mir-486_5p","Hsa-Mir-488_3p","Hsa-Mir-489-v1_3p","Hsa-Mir-489-v2_3p","Hsa-Mir-490_5p","Hsa-Mir-491_5p","Hsa-Mir-493_5p","Hsa-Mir-499_5p","Hsa-Mir-504-v1_5p","Hsa-Mir-504-v2_5p","Hsa-Mir-505-v1_5p","Hsa-Mir-505-v2_5p","Hsa-Mir-506-P1_5p","Hsa-Mir-506-P1_3p","Hsa-Mir-506-P2_3p","Hsa-Mir-506-P3_3p","Hsa-Mir-506-P4a1_3p","Hsa-Mir-506-P4a2_3p","Hsa-Mir-506-P4b_3p","Hsa-Mir-506-P5_5p","Hsa-Mir-506-P6a1_5p","Hsa-Mir-506-P6a2_5p","Hsa-Mir-506-P6b_5p","Hsa-Mir-506-P6c_5p","Hsa-Mir-506-P7a_3p","Hsa-Mir-506-P7b_3p","Hsa-Mir-506-P7c_3p","Hsa-Mir-506-P8_5p","Hsa-Mir-506-P9_5p","Hsa-Mir-506-P10_5p","Hsa-Mir-506-P11_3p","Hsa-Mir-506-P12_3p","Hsa-Mir-506-P13_5p","Hsa-Mir-506-P13_3p","Hsa-Mir-506-P29_3p","Hsa-Mir-511_5p","Hsa-Mir-511_3p","Hsa-Mir-541_5p","Hsa-Mir-541_3p","Hsa-Mir-542-v1_3p","Hsa-Mir-542-v2_3p","Hsa-Mir-544_3p","Hsa-Mir-550-P1_3p","Hsa-Mir-550-P2a_3p","Hsa-Mir-550-P2b_3p","Hsa-Mir-551-P1_3p","Hsa-Mir-551-P2_3p","Hsa-Mir-552_5p","Hsa-Mir-552_3p","Hsa-Mir-556_5p","Hsa-Mir-556_3p","Hsa-Mir-561_5p","Hsa-Mir-574_3p","Hsa-Mir-576_5p","Hsa-Mir-577_5p","Hsa-Mir-579_3p","Hsa-Mir-580_3p","Hsa-Mir-582-v1_5p","Hsa-Mir-582-v2_5p","Hsa-Mir-584_5p","Hsa-Mir-585_3p","Hsa-Mir-589_5p","Hsa-Mir-590_3p","Hsa-Mir-592_5p","Hsa-Mir-598_3p","Hsa-Mir-599_5p","Hsa-Mir-605-v1_3p","Hsa-Mir-605-v2_3p","Hsa-Mir-615_3p","Hsa-Mir-616_5p","Hsa-Mir-624_5p","Hsa-Mir-628_5p","Hsa-Mir-628_3p","Hsa-Mir-629_5p","Hsa-Mir-642_5p","Hsa-Mir-651_5p","Hsa-Mir-652_3p","Hsa-Mir-653_3p","Hsa-Mir-670_3p","Hsa-Mir-671_5p","Hsa-Mir-671_3p","Hsa-Mir-675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"ERR409886",18482,47783,208285,208285,208285,129115,129115,27498,21535,7913,16405,45477,89,1,89,1932,1932,1932,381,46,389,349,466,162369,8029,162369,8029,162369,8029,33274,2402,3269,551,84391,22426,52166,181833,85271,85271,3166,363,352,2111,36647,37811,20,5760,662,164,473,254,104,28,884,163,3226,399,1216,1216,21918,4210,9845,3637,3329,3329,1006516,30890,1006516,163575,11134,1438,14574,29328,6468,1337,6548,2989,6548,2989,43894,11586,79701,187929,81149,14185,36070,36070,949,293,433,323,967,79,17,589,7,8,7,0,16,22290,22290,78218,1,2416,5989,994,2462,10,8,4,25,217,7399,1483,590,40121,31860,40121,31860,7270,35489,35489,78,78,5,41977,52733,41977,52733,41977,52733,24196,106512,25090,128705,72327,72327,2106,3709,546,4454,518,3843,1086,190,287,6120,302,753,1559,508,52,9,1559,508,720,1351,1351,8,9448,1723,1608,2194,254,11997,11997,6497,4501,8186,1835,76,367,2979,620467,1162,1282,7301,17722,967,4,5,11049,191,3009,10014,1904,11572,11572,268,20,85,59,1103,2084,1134,502,502,367,493,450,432,27,209,11651,412,7405,9289,20935,92,840,462,2164,87,424,19,18,1622,309,4200,62,379,515,2947,18,355,4,0,149,3582,695,392597,392597,43191,22462,22462,5225,141,285,25940,79,26,1276,1129,2275,18,119626,902,8147,410,177,74,465,574,580,16,12,19,6654,3161,3637,359,3161,3637,359,3161,3637,359,0,370,90,174,18936,9,56,1,456,79,121,0,0,0,3,3644,3644,2830,1575,354,2139,4,11573,888,17482,869,122,20,2912,284,284,74,79,597,0,73,327,750,960,920,4664,1975,2,10,10,35,24,63,21870,21979,248,96,1043,8654,6748,1105,247,2537,1202,196,1259,987,711,213,23,609,804,1278,863,373,217,37,217,911,4,7172,266,313,3003,8642,2484,2,1,7,6,0,3,1,4,0,0,3,0,3,0,4,3,0,2,0,8,23,2,2,1,3,0,2,2,1,0,0,0,0,0,0,127,127,20,1,2,2,3,0,0,30,0,0,6,0,0,0,0,3,8,8,16,27,1650,1122,3,7,98,98,181,9006,41,36,263,0,84,21802,607,25,3,26,70,36,132,672,582,5,0,0,1,0,5,13,13,13,0,1,1,0,2,2,2,2,0,6,1,7,0,0,1,0,8,6,9,12,42,36,6,57,57,57,6,63,2,2,2,0,90,1141,70,1294,0,6,280,125,610,3,333,83,188,2777,0,2,0,10,17,6,847,372,63,3,33,178,1,62,78,443,7,1,4015,21,274,20009,470,1630,309,1077,2891,2,38,192,1026,22,841,944,975,2,1489,126,914,77,19,0,3,7,799,0,9,76,1,36,17,1,1,2648,284,370,49,9072,1,32,21,0,40,18,1,4,1,9,6,9,1,5,0,1,38,1,163,74,8,0,13,1,2,0,0,0,0,0,4,1,16,16,16,0,6,719,14,143,2,1,8,16,0,4,74,0,1,0,1,0,0,10,0,0,0,44,0,1,33,0,1,0,2,0,0,4,23,427,0,0,1,0,3,4,0,1,2,1
"ERR409894",25295,74145,314056,314056,314056,196868,196868,44708,38319,12313,25733,73578,80,0,80,2544,2544,2544,60,12,52,47,23,296685,5669,296685,5669,296685,5669,61620,4875,1558,331,41100,14486,30986,81252,66568,66568,4681,473,316,3132,43675,45066,17,4206,806,114,446,364,131,17,1169,170,4443,296,1181,1181,16810,3742,11247,2053,3471,3471,1077711,36069,1077711,251199,4538,962,10434,38256,15234,1483,9233,3091,9233,3091,40611,13395,112919,181079,77627,20833,38564,38564,1215,336,1173,523,1588,102,15,992,11,20,2,0,18,35052,35052,64729,0,1835,7599,1128,4416,11,9,2,24,9,1411,50,26,49727,59678,49727,59678,12143,60887,60887,146,146,24,59511,69508,59511,69508,59511,69508,13765,73971,14378,181488,87393,87393,2443,7258,857,3754,448,6669,1345,93,269,10423,319,828,1134,372,39,2,1134,372,1886,1296,1296,8,16570,2736,1479,2334,206,28543,28543,8033,4699,8944,1127,44,190,1110,197946,893,1024,3502,25612,1136,15,16,6976,173,3722,16591,1010,12486,12486,349,73,118,109,2897,4897,1953,747,747,887,868,455,1055,34,233,7366,1364,27279,17203,36872,35,1618,1180,3475,225,637,42,75,2579,264,2381,142,595,1042,5190,79,896,8,0,303,10352,306,1210291,1210291,62245,81344,81344,7834,212,430,25963,115,26,1259,1342,2729,17,135192,941,8565,694,243,67,359,519,532,12,11,16,4628,1120,1313,122,1120,1313,122,1120,1313,122,0,669,143,13,12255,5,126,0,575,15,19,0,9,4,3,5260,5260,10450,8358,2101,7874,2,16851,496,23335,301,31,33,3306,433,433,113,116,1079,0,93,471,1467,1740,1499,3550,1611,2,3,3,47,16,69,60609,60760,352,154,1462,32764,6652,1518,385,2464,1797,137,985,829,292,114,22,979,940,2096,931,1010,278,35,278,1288,0,5042,699,901,2677,6997,4201,7,4,8,6,0,0,0,4,1,1,6,0,6,0,3,0,0,1,0,18,20,1,1,2,2,2,0,0,0,0,0,0,0,1,1,123,123,2,1,2,2,4,2,2,16,0,0,14,0,0,0,1,0,9,9,76,90,3853,2099,0,6,99,99,210,17440,7,5,161,1,11,20637,1413,30,7,91,175,59,227,607,568,10,2,0,1,0,10,13,13,13,0,4,4,1,7,16,16,16,0,0,0,5,0,0,1,0,7,2,11,66,112,51,8,29,29,29,2,76,5,0,1,1,25,813,60,3218,2,3,469,238,2573,1,597,92,615,4342,0,0,0,8,18,1,1402,444,54,7,57,253,6,136,151,705,1,7,8443,48,226,59904,413,3923,880,2508,4247,0,59,464,1511,24,1237,1708,1775,0,2620,103,1958,183,15,4,6,10,225,2,13,75,0,55,55,1,0,2771,95,435,80,13812,5,59,56,0,9,3,1,4,3,4,2,16,0,7,1,9,38,3,352,163,37,0,12,0,0,0,0,0,0,2,6,0,8,8,8,5,0,1544,11,384,2,0,18,10,5,0,94,0,0,0,2,0,2,11,2,0,2,69,0,0,104,2,0,1,0,0,0,7,6,497,0,1,0,9,20,4,2,2,0,1
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"ERR409883",50124,117559,287216,287216,287216,150966,150966,100340,51970,9076,78984,50759,302,0,302,40367,40367,40367,181,26,225,201,59,1119735,27361,1119735,27361,1119735,27361,5018,316,3471,687,468097,64336,91004,268350,354990,354990,4998,284,895,4963,42614,44550,96,13652,1311,292,2499,2068,649,105,1269,469,10365,817,5402,5402,33324,10176,13571,5281,23971,23971,1911607,44636,1911607,407620,23050,1703,19193,33314,46720,8424,35669,11189,35669,11189,171798,57777,349596,563598,335059,32911,69221,69221,2883,491,1586,3812,4965,74,21,802,11,14,11,1,63,39084,39084,76677,0,3661,12219,3110,4234,19,17,16,268,56,3398,2523,1335,147985,189832,147985,189832,37333,208477,208477,571,571,35,498334,612748,498334,612748,498334,612748,62043,168531,63733,2090432,269080,269080,20258,64162,4986,13149,1937,7467,934,340,1205,20602,3495,2896,7158,2419,991,58,7158,2419,11113,3078,3078,65,47726,7408,14128,29901,1870,74909,74909,40377,19877,28272,3074,131,581,3413,1060230,1685,1921,10765,156907,14390,67,77,16279,1124,32150,77904,1688,51619,51619,1586,379,256,276,9602,13797,7483,4254,4254,704,1731,2030,9343,318,493,26271,6867,40611,18954,35032,817,4894,1261,6952,343,4678,122,152,1793,1535,7937,1151,780,5730,5347,169,1856,31,3,1592,29631,951,427957,427957,100468,66958,66958,20062,957,2401,52335,968,69,6524,3906,4684,25,650151,1497,23833,3063,529,471,1168,856,875,5,0,0,15747,2042,2337,221,2042,2337,221,2042,2337,221,1,3725,689,1400,50953,17,319,0,1971,87,137,9,57,10,11,20344,20344,22926,10814,5018,16382,3,61170,2346,87707,538,7,24,23708,4792,4792,1507,1515,4305,0,497,3006,4138,6203,10836,19210,6120,8,36,36,71,80,133,57358,57586,701,1067,3959,60034,63126,2948,1604,7940,5494,1473,2578,1889,1300,582,84,11665,2101,2616,1650,1248,2230,210,2230,11983,18,28375,1408,1585,6434,11302,11004,2,0,5,9,10,1,5,35,2,2,6,0,6,0,6,7,3,11,3,30,109,11,11,1,2,1,6,6,0,0,2,0,0,4,4,532,532,21,4,3,3,0,10,10,63,0,3,50,2,3,3,0,12,12,12,140,531,14287,7284,24,89,280,280,351,16557,24,27,941,0,72,48819,5988,36,1,661,2194,145,641,5311,4509,2,0,0,3,2,45,108,108,108,4,3,3,0,2,13,13,13,1,7,6,5,0,0,0,0,8,16,99,97,507,326,42,101,101,101,13,438,22,35,7,4,246,1742,48,3985,3,13,1169,1035,3764,14,1101,78,1212,8978,0,0,0,1,41,5,1220,750,467,14,131,1110,21,266,1341,1691,22,7,31197,422,1714,379207,2475,32833,10260,21435,34460,0,320,840,4514,122,3861,3534,3761,3,5786,255,2912,2242,63,18,42,39,174,12,69,147,0,512,114,2,14,16093,223,2379,219,96360,2,192,70,1,29,57,7,55,8,38,19,36,4,12,0,7,91,19,1664,386,142,3,46,0,0,0,0,0,0,0,4,2,158,158,158,6,10,5946,72,632,18,4,62,18,6,26,159,0,28,2,4,0,12,24,1,0,0,39,3,0,250,1,4,0,2,1,2,26,21,5035,3,3,0,3,5,8,0,0,1,3
"ERR409900",114606,271460,1258967,1258967,1258967,802974,802974,174495,142624,55680,97566,310818,449,2,449,20439,20439,20439,164,45,140,90,82,1160019,26481,1160019,26481,1160019,26481,1784,136,2827,530,223093,54743,131887,378490,235292,235292,16596,1905,1287,13171,177881,182861,44,23195,2793,575,1619,997,455,66,4785,876,19463,772,3276,3276,49412,16041,39170,8280,13975,13975,2066195,124098,2066195,999775,18861,3739,36351,153639,45029,5772,28289,10093,28289,10093,127958,41609,403791,585382,311134,71196,161776,161776,6805,1286,3451,1312,7548,408,84,2460,20,34,14,0,36,108578,108578,300449,0,7367,27213,4329,18039,51,37,36,118,58,3342,186,103,134743,168965,134743,168965,47477,252692,252692,535,535,69,150302,181910,150302,181910,150302,181910,46629,260473,49065,602166,333051,333051,12122,33485,4616,14620,2601,24631,5466,458,1361,60706,1678,5030,5166,1492,167,5,5166,1492,4476,9489,9489,148,58020,8347,5435,8629,1034,115714,115714,35419,19893,35601,4710,210,830,4827,497102,2252,2510,9263,134204,5168,23,29,19534,483,13217,53480,4833,43066,43066,1315,184,585,553,8569,14720,8291,2470,2470,3515,3396,1706,3964,70,1106,42961,4609,109192,64366,150646,123,5312,5111,14033,661,3690,215,296,10706,1698,10548,437,2398,3018,20627,214,3808,26,2,1150,33478,1115,4350668,4350668,228499,320102,320102,27194,689,2334,87752,665,101,3461,3804,10323,25,500036,3042,26345,2294,909,428,1924,1708,1737,9,1,3,20189,3434,4117,338,3434,4117,338,3434,4117,338,0,2537,615,1928,41926,32,318,1,1816,84,118,9,12,4,19,17955,17955,29759,32651,8088,21118,7,84282,3645,90702,1322,46,84,13284,1725,1725,672,681,3642,0,298,1480,5476,6658,5486,15309,8632,8,44,44,169,133,259,213137,213856,1507,336,4280,94473,28328,5058,1296,8817,5286,662,4059,3497,1270,386,91,4071,3045,5972,3084,2991,946,156,946,4217,18,21283,3045,3766,11448,27542,15958,11,1,4,10,5,1,8,17,0,0,10,0,10,0,9,4,1,2,0,21,55,2,2,3,4,0,0,0,1,0,4,1,1,2,2,192,192,9,1,6,6,0,2,2,50,0,3,12,2,1,1,2,3,9,9,367,316,12500,8927,23,37,395,395,763,62895,38,23,631,0,21,76857,4194,166,17,228,449,240,651,2017,1856,29,7,1,1,0,43,43,43,43,1,8,8,0,15,32,32,32,0,15,1,20,4,1,1,0,30,9,62,171,338,200,50,201,201,201,4,178,15,10,17,11,165,4232,262,17181,0,28,1533,714,11392,33,1782,303,2428,13519,1,0,0,2,81,15,4184,1386,164,50,146,694,10,887,646,2322,8,25,32413,158,1081,193939,1838,9853,2269,6412,14719,0,278,1590,7838,124,5040,6012,6372,5,9394,206,4752,975,97,8,24,53,1716,3,60,336,9,254,126,15,12,8235,482,2372,200,42483,1,315,261,1,6,39,2,4,5,19,19,52,4,29,2,14,282,12,951,664,73,3,49,5,0,1,1,0,2,2,26,10,52,52,52,4,7,5746,39,893,7,2,97,25,17,13,415,0,2,0,4,1,3,71,2,0,1,207,1,0,353,0,2,1,1,0,1,39,115,2549,0,0,1,22,16,16,0,1,2,1

cp /work/training/2024/smallRNAseq/scripts/transpose_csv.py .

python transpose_csv.py --help

usage: transpose_csv.py [-h] --input INPUT --output OUTPUT
Transpose a CSV file and generate a tab-delimited TXT file.
optional arguments:
  -h, --help       show this help message and exit
  --input INPUT    Input CSV file containing mature miRNA counts.
  --output OUTPUT  Output tab-delimited TXT file.

python transpose_csv.py --input mature_counts.csv --out mature_counts.txt

cat mature_counts.txt

microRNA	ERR409886	ERR409894	ERR409882	ERR409895	ERR409889	ERR409899	ERR409879	ERR409885	ERR409881ERR409884	ERR409887	ERR409896	ERR409891	ERR409880	ERR409878	ERR409898	ERR409897	ERR409893	ERR409890ERR409892	ERR409888	ERR409883	ERR409900
Hsa-Let-7-P1b_5p	18482	25295	29486	51987	44172	26036	23604	46550	68044	13902	15724	33998	29525	24585	29935	15501	19495	39737	31807	20070	20686	50124	114606
Hsa-Let-7-P1c_5p	47783	74145	68342	118227	100021	66085	58426	128501	162724	39989	41506	84952	75858	65606	69995	41283	46267	86159	73537	62698	53365	117559	271460
Hsa-Let-7-P1d_5p	208285	314056	364624	531423	568283	289927	305660	546059	712891	182180	178203	421398	351589	318124	432959	186915	242780	417695	332584	249356	320237	287216	1258967
Hsa-Let-7-P2a1_5p	208285	314056	364624	531423	568283	289927	305660	546059	712891	182180	178203	421398	351589	318124	432959	186915	242780	417695	332584	249356	320237	287216	1258967
Hsa-Let-7-P2a2_5p	208285	314056	364624	531423	568283	289927	305660	546059	712891	182180	178203	421398	351589	318124	432959	186915	242780	417695	332584	249356	320237	287216	1258967
Hsa-Let-7-P2a3_5p	129115	196868	211190	425095	276482	223463	198784	376491	456871	127391	123392	276681	231752	191076	250199	126873	155636	288225	207846	133797	154352	150966	802974
Hsa-Let-7-P2b1_5p	129115	196868	211190	425095	276482	223463	198784	376491	456871	127391	123392	276681	231752	191076	250199	126873	155636	288225	207846	133797	154352	150966	802974
Hsa-Let-7-P2b2_5p	27498	44708	59417	75630	92339	43602	52115	59795	83857	27892	25678	45870	37230	46347	61357	25897	28396	62467	40131	28694	56350	100340	174495
Hsa-Let-7-P2b3_5p	21535	38319	50824	54780	45533	31044	30986	58479	80694	21549	21471	45473	42277	33601	48053	22597	25577	46855	39626	25804	35260	51970	142624
Hsa-Let-7-P2c1_5p	7913	12313	14861	27318	20819	14122	12397	22746	30556	7751	7833	17317	14405	11095	15326	8698	10109	19831	13528	9305	10690	9076	55680
Hsa-Let-7-P2c2_5p	16405	25733	35925	46007	40731	26046	31814	52245	48422	22131	16863	28264	28404	30137	36839	16318	21184	38978	27316	15145	24807	78984	97566
Hsa-Let-7-P2c3_5p	45477	73578	72845	123354	109175	74340	71170	128485	173832	46596	39681	98399	83319	68711	96580	47999	55668	104358	82526	41838	53362	50759	310818
Hsa-Mir-1-P1_3p	89	80	74	94	90	52	118	226	236	66	47	190	181	97	118	57	79	187	123	24	33	302	449
Hsa-Mir-1-P2_3p	1	0	0	0	2	0	0	0	4	2	0	0	1	0	0	0	0	22
Hsa-Mir-1-P3_3p	89	80	74	94	90	52	118	226	236	66	47	190	181	97	118	57	79	187	123	24	33	302	449
Hsa-Mir-7-P1_5p	1932	2544	2622	2601	3681	1065	2172	3395	7532	1447	851	3483	3044	2989	3100	1450	1927	4548	4122	1976	1368	40367	20439
Hsa-Mir-7-P2_5p	1932	2544	2622	2601	3681	1065	2172	3395	7532	1447	851	3483	3044	2989	3100	1450	1927	4548	4122	1976	1368	40367	20439
Hsa-Mir-7-P4_5p	1932	2544	2622	2601	3681	1065	2172	3395	7532	1447	851	3483	3044	2989	3100	1450	1927	4548	4122	1976	1368	40367	20439
Hsa-Mir-8-P1a_3p	381	60	131	86	128	64	50	98	111	35	49	64	51	47	121	46	462	86	139	66	181	164
Hsa-Mir-8-P1b_3p	46	12	9	29	27	21	11	26	38	7	5	26	21	25	18	16	115	16	25	6	26	45
Hsa-Mir-8-P2a_3p	389	52	77	46	182	48	77	67	68	36	39	23	39	36	117	43	347	51	44	44	225	140
Hsa-Mir-8-P2b_3p	349	47	40	64	73	33	45	93	83	34	25	40	48	50	56	20	435	49	81	21	201	90
Hsa-Mir-8-P3a_3p	466	23	61	25	63	23	32	38	29	16	19	25	19	44	76	20	126	40	27	16	59	82
Hsa-Mir-9-P1_5p	162369	296685	325973	351690	348083	202181	244049	538146	505079	196178	145191	338071	320620	290747	375141	143367	221771	352483	313212	190994	160209	1119735	1160019
Hsa-Mir-9-P1_3p	8029	5669	8439	8239	12697	5564	6070	13606	11707	4898	4103	7300	7883	8820	7685	4557	5025	7405	9454	10681	4621	27361	26481
Hsa-Mir-9-P2_5p	162369	296685	325973	351690	348083	202181	244049	538146	505079	196178	145191	338071	320620	290747	375141	143367	221771	352483	313212	190994	160209	1119735	1160019
Hsa-Mir-9-P2_3p	8029	5669	8439	8239	12697	5564	6070	13606	11707	4898	4103	7300	7883	8820	7685	4557	5025	7405	9454	10681	4621	27361	26481
Hsa-Mir-9-P3_5p	162369	296685	325973	351690	348083	202181	244049	538146	505079	196178	145191	338071	320620	290747	375141	143367	221771	352483	313212	190994	160209	1119735	1160019
Hsa-Mir-9-P3_3p	8029	5669	8439	8239	12697	5564	6070	13606	11707	4898	4103	7300	7883	8820	7685	4557	5025	7405	9454	10681	4621	27361	26481
Hsa-Mir-10-P1b-v1_5p	33274	61620	590	20151	10343	7551	745	6828	33515	6965	653	1120	1043	46880	1104	315	30186	937	12711	12178	603	5018	1784
Hsa-Mir-10-P1b-v2_5p	2402	4875	39	1621	815	621	53	446	2722	504	47	90	75	3480	84	26	2067	70	916	810	38	316	136
Hsa-Mir-10-P1c-v1_5p	3269	1558	257	1767	896	405	556	6232	33628	726	1175	1313	599	2808	1498	287	686	1232	1025	3019	773	3471	2827
Hsa-Mir-10-P1c-v2_5p	551	331	40	374	173	69	81	906	6418	106	194	246	98	551	288	45	125	230	192	549	135	687	530
Hsa-Mir-10-P2b_5p	84391	41100	76456	45448	114204	53057	39073	64175	83922	43204	32872	38187	55062	69417	39121	25110	22826	65593	70976	58992	55847	468097	223093
Hsa-Mir-10-P2c_5p	22426	14486	15965	16006	25485	14763	13513	23895	33096	12728	9571	12327	15968	20179	13461	8407	8378	15562	18562	24577	11674	64336	54743
Hsa-Mir-10-P2d_5p	52166	30986	79481	28319	107620	40535	37070	60082	63987	30825	18025	28735	39781	44661	44899	20461	14628	41072	40955	38033	53908	91004	131887
Hsa-Mir-10-P3b_5p	181833	81252	138889	126317	224474	111938	83880	192590	206640	68002	66334	106078	137101	131928	88529	64913	62802	124192	140567	180845	87696	268350	378490
Hsa-Mir-10-P3c_5p	85271	66568	79205	77580	124928	63693	61766	105925	140562	44846	40183	57630	69745	78369	66116	41947	36981	73506	80308	103672	61217	354990	235292
Hsa-Mir-10-P3d_5p	85271	66568	79205	77580	124928	63693	61766	105925	140562	44846	40183	57630	69745	78369	66116	41947	36981	73506	80308	103672	61217	354990	235292
Hsa-Mir-15-P1a_5p	3166	4681	7002	12518	12407	5151	5486	7931	9893	3651	3288	5614	4055	5599	9213	3567	3704	5804	5146	4126	4751	4998	16596
Hsa-Mir-15-P1b_5p	363	473	516	719	857	312	563	822	1007	471	295	474	465	715	823	300	306	478	376	418	527	284	1905
Hsa-Mir-15-P1c_5p	352	316	560	205	511	120	250	567	557	282	115	277	305	289	572	111	197	282	297	354	386	895	1287
Hsa-Mir-15-P1d_5p	2111	3132	2437	6701	3326	3637	2450	3479	7965	2261	2204	3698	2989	3168	2864	1994	2213	4398	3161	3333	1869	4963	13171
Hsa-Mir-15-P2a_5p	36647	43675	49659	106970	83889	50438	48372	73527	111687	40310	39428	55347	45421	67394	73290	34801	35131	54599	42388	49614	56121	42614	177881
Hsa-Mir-15-P2b_5p	37811	45066	51704	108410	86937	51359	49837	76507	114249	41613	40251	57207	47166	69275	76485	35712	36475	55968	43780	51047	57923	44550	182861
Hsa-Mir-15-P2c_5p	20	17	8	17	22	5	10	22	34	13	3	9	17	17	17	10	911	20	16	18	96	44
Hsa-Mir-15-P2d_5p	5760	4206	4855	8138	6641	3753	4989	8525	12105	6397	3595	6472	6607	8438	7082	3257	4859	5490	5432	6714	4529	13652	23195
Hsa-Mir-17-P1a_5p	662	806	1091	822	1971	548	945	1079	1495	629	445	681	666	1242	1301	537	561	805	659	590	934	1311	2793
Hsa-Mir-17-P1c_5p	164	114	99	159	191	83	71	125	304	88	43	104	83	249	128	63	128	131	146	82	62	292	575
Hsa-Mir-17-P1d_5p	473	446	857	1033	1318	436	573	866	850	412	400	554	355	731	853	413	358	549	559	439	510	2499	1619
Hsa-Mir-17-P1d_3p	254	364	419	814	579	381	324	428	490	226	277	302	229	350	391	218	262	349	299	189	403	2068	997
Hsa-Mir-17-P2a_5p	104	131	326	101	403	76	194	137	174	97	65	98	104	168	327	85	7115	102	69	222	649	455
Hsa-Mir-17-P2c_5p	28	17	29	18	48	18	13	20	34	13	11	20	18	41	27	7	112	30	16	15	105	66
Hsa-Mir-17-P4a_5p	884	1169	1615	1036	3172	855	1317	1632	2220	902	461	1097	1199	1836	2163	673	869	1156	1086	649	1176	1269	4785
Hsa-Mir-17-P4c_5p	163	170	144	215	257	111	84	168	469	124	62	173	136	309	189	67	158	214	209	88	93	469	876
Hsa-Mir-17-P4d_5p	3226	4443	6901	8262	9831	3914	5416	5275	7821	3750	2768	4263	3474	5608	7290	2739	2781	5811	3821	2346	6879	10365	19463
Hsa-Mir-19-P1a_3p	399	296	468	307	1082	232	368	473	318	305	150	237	298	505	542	253	259	247	219	346	358	817	772
Hsa-Mir-19-P2a_3p	1216	1181	1482	1046	3082	766	1097	1656	1466	1147	539	878	1054	1708	1773	788	912	884	964	1312	1284	5402	3276
Hsa-Mir-19-P2c_3p	1216	1181	1482	1046	3082	766	1097	1656	1466	1147	539	878	1054	1708	1773	788	912	884	964	1312	1284	5402	3276
Hsa-Mir-21_5p	21918	16810	24378	23678	33803	20854	17441	28742	25992	11326	7940	22008	20342	16238	29409	10725	13724	17677	18528	13654	14586	33324	49412
Hsa-Mir-22-P1b_3p	4210	3742	6526	9282	6428	4826	3693	7321	10360	2276	2958	5011	4172	3652	4830	3335	2297	6177	6017	5602	3041	10176	16041
Hsa-Mir-23-P2_3p	9845	11247	17222	11499	14994	6013	11852	14345	16971	10756	9108	12375	14864	12411	28226	9190	7116	12957	8092	18031	28252	13571	39170
Hsa-Mir-23-P3_3p	3637	2053	2551	3093	2989	1923	1912	4189	4722	1657	1310	2482	2937	3303	3081	1396	1721	2606	2176	3275	2087	5281	8280
Hsa-Mir-24-P2_3p	3329	3471	5206	2510	6773	2039	4549	4608	6172	2715	1544	2830	2943	4085	5937	3148	1886	3436	3320	3630	3465	23971	13975
Hsa-Mir-24-P3_3p	3329	3471	5206	2510	6773	2039	4549	4608	6172	2715	1544	2830	2943	4085	5937	3148	1886	3436	3320	3630	3465	23971	13975
Hsa-Mir-26-P1_5p	1006516	1077711	912248	890275	1126662	568618	648819	1234738	1306207	444239	468744	808800	928138	992232	1475541	523073	559600	692502	880724	1170207	839104	1911607	2066195
Hsa-Mir-26-P2_5p	30890	36069	41809	42091	67728	28058	37424	71349	64732	24388	18438	40245	36161	47704	56249	22951	26013	36812	34280	33901	33080	44636	124098
Hsa-Mir-26-P4_5p	1006516	1077711	912248	890275	1126662	568618	648819	1234738	1306207	444239	468744	808800	928138	992232	1475541	523073	559600	692502	880724	1170207	839104	1911607	2066195
Hsa-Mir-27-P2_3p	163575	251199	483786	330699	646255	237548	386589	340718	456521	233163	136266	283426	222559	251724	638569	177823	176044	336033	248387	172564	422947	407620	999775
Hsa-Mir-27-P3_3p	11134	4538	6316	11208	8880	7110	6048	10429	11564	4314	3946	7213	5353	7333	8045	4711	4313	7001	7578	8606	4270	23050	18861
Hsa-Mir-28-P1_5p	1438	962	1189	3235	2113	1522	1002	2937	2762	713	798	1705	1285	1138	1421	826	943	1459	1316	1527	894	1703	3739
Hsa-Mir-28-P1_3p	14574	10434	9908	25120	17403	12641	8493	20984	22652	5836	5997	12424	12393	12443	12565	4986	7353	12725	11128	9062	8432	19193	36351
Hsa-Mir-28-P2_5p	29328	38256	69875	55300	108618	47514	51180	55486	74781	29302	26416	44621	34429	37379	72979	34109	26047	51962	42063	38068	57885	33314	153639
Hsa-Mir-28-P2_3p	6468	15234	25710	14939	35513	11334	17850	19264	18176	9379	6398	13050	9831	11713	24988	6739	9175	15407	12966	7155	20470	46720	45029
Hsa-Mir-28-P3_5p	1337	1483	1943	1113	1909	763	1537	2643	2515	1419	1089	1245	1553	1502	1909	1048	848	1801	1498	2654	1302	8424	5772
Hsa-Mir-29-P1b-v1_3p	6548	9233	9231	7204	18075	4033	10383	18227	16612	7804	3548	6990	9338	12501	9461	5152	6062	8918	11360	7076	3688	35669	28289
Hsa-Mir-29-P1b-v2_3p	2989	3091	3800	3802	5576	2351	3578	7360	6025	2854	1926	2931	3390	4447	3581	2432	2387	2846	4032	4117	2158	11189	10093
Hsa-Mir-29-P1d-v1_3p	6548	9233	9231	7204	18075	4033	10383	18227	16612	7804	3548	6990	9338	12501	9461	5152	6062	8918	11360	7076	3688	35669	28289
Hsa-Mir-29-P1d-v2_3p	2989	3091	3800	3802	5576	2351	3578	7360	6025	2854	1926	2931	3390	4447	3581	2432	2387	2846	4032	4117	2158	11189	10093
Hsa-Mir-29-P2b_3p	43894	40611	47851	60529	67338	32490	40318	87923	86030	31781	24682	40846	39369	43362	43606	30538	27862	41001	52719	64033	26618	171798	127958
Hsa-Mir-29-P2d_3p	11586	13395	16570	19337	23043	9869	13317	28764	27061	10062	7965	14105	14032	14217	14330	9693	9690	13547	16568	18645	8055	57777	41609
Hsa-Mir-30-P1a_5p	79701	112919	97895	141169	120517	88055	76955	157223	225215	57601	63546	110045	110091	100389	115458	56006	65757	124821	105362	101044	77062	349596	403791
Hsa-Mir-30-P1b_5p	187929	181079	154770	275225	282422	133689	153308	400714	388430	128120	98963	196102	201672	262121	206834	76514	156644	202675	219067	139165	101046	563598	585382
Hsa-Mir-30-P1d_5p	81149	77627	94091	119188	152861	69828	75424	156264	183906	64357	51187	96291	103617	103390	104392	53593	67159	95959	104021	77035	55954	335059	311134
Hsa-Mir-30-P2a_5p	14185	20833	19681	21785	22050	12162	16435	37164	40028	12170	10449	20531	20408	22148	21349	9002	13257	18881	22854	19332	13633	32911	71196
Hsa-Mir-30-P2b_5p	36070	38564	46605	79221	61147	44997	34395	89158	95562	23331	24714	50059	51940	48346	45494	23380	32108	54920	47955	44324	26101	69221	161776
Hsa-Mir-30-P2d_5p	36070	38564	46605	79221	61147	44997	34395	89158	95562	23331	24714	50059	51940	48346	45494	23380	32108	54920	47955	44324	26101	69221	161776
Hsa-Mir-31_5p	949	1215	1564	2112	1607	1396	1339	2686	3318	1531	1199	1243	1547	1283	1492	1219	1063	1899	1369	1313	873	2883	6805
Hsa-Mir-32_5p	293	336	824	604	1123	324	539	663	651	344	205	450	333	575	895	305	247	431	356	267	354	491	1286
Hsa-Mir-33-P1_5p	433	1173	2449	1384	4399	927	1858	985	1114	737	446	775	350	793	2830	949	653	1175	893	337	1031	1586	3451
Hsa-Mir-33-P3_5p	323	523	616	493	1112	253	521	462	632	298	179	310	209	458	787	263	294	494	481	332	166	3812	1312
Hsa-Mir-34-P1_5p	967	1588	1556	1645	2428	1377	1840	2643	4042	1174	910	1797	1995	1732	1737	1376	924	2212	1860	1222	683	4965	7548
Hsa-Mir-34-P2a_5p	79	102	253	82	238	73	206	145	102	90	49	106	73	77	373	61	6136	58	52	177	74	408
Hsa-Mir-34-P2a_3p	17	15	56	16	34	21	44	14	34	16	10	18	12	15	54	13	739	9	17	56	21	84
Hsa-Mir-34-P2b_5p	589	992	1597	611	1228	475	1403	678	751	520	417	807	405	310	2047	509	305	1064	275	390	1336	802	2460
Hsa-Mir-34-P3a-v1_5p	7	11	6	5	16	12	8	17	13	14	6	11	11	13	5	7	811	20
Hsa-Mir-34-P3a-v2_5p	8	20	14	23	19	24	12	31	28	26	15	18	25	16	6	10	221	20	6	14	34
Hsa-Mir-34-P3b_5p	7	2	2	10	16	7	25	5	7	7	11	7	10	7	3	1	912	2	11	14
Hsa-Mir-34-P3b_3p	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	00