6.5 Huntington Disease samples profiling against MirGeneDB curated database
- Roberto Barrero Gumiel
Owned by Roberto Barrero Gumiel
Overview
Similar to exercise 6.4 we will:
Use created “samplesheet.csv” metadata file for small RNAseq datasets in exercise 6.4.
Use a “nextflow.config” file in the working directory to override Nextflow parameters (e.g., specify where to find the pipeline assets).
Use a PBS script to run the expression profiling of miRNAs against MirGeneDB, a curated database that includes experimentally validated miRNAs.
Prepare pipeline inputs
Let’s move to the working directory:
cd $HOME/workshop/2024-2/session6_smallRNAseq/runs/run2_human_MirGeneDBNow, let’s copy the samplesheet.csv, nextflow.config and the PBS script to run the pipeline agains MirGeneDB files:
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 .Print the content of the launch script:
cat launch_nf-core_smallRNAseq_MirGeneDB.pbs
Submit the job to the HPC cluster:
qsub launch_nf-core_smallRNAseq_MirGeneDB.pbsMonitor the progress:
qjobsThe job will take several hours to run, hence we will use precomputed results for the statistical analysis in the next section.
Outputs
The pipeline will produce two folders, one called “work,” where all the processing is done, and another called “results,” where we can find the pipeline's outputs. The content of the results folder is as follows:
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.htmlThe quantification of the mature miRNA and hairpin expressions can be found in the /results/mirna_quant/edger_qc directory.
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.txtLet’s inspect the mature.csv file. Let’s use the ‘cat’ command to print it on the screen:
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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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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Let’s copy the transpose_csv.py script to the working folder:
cp /work/training/2024/smallRNAseq/scripts/transpose_csv.py .The check how to use the script do the following:
python transpose_csv.py --helpusage: 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.To transpose the initial “mature_counst.csv” file do the following:
python transpose_csv.py --input mature_counts.csv --out mature_counts.txtLet’s now print the transposed mature counts table:
cat mature_counts.txtmicroRNA 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