...
(2) HCT116 WT cells cultured with media supplemented with 9.1 % or 0.1 % FBS.
Sample metadata:
sample | group | treatment | cell | replicate |
SRR24302008 | WT | 0.1 % FBS, 72 hr | HCT116 | rep3 |
SRR24302009 | WT | 0.1 % FBS, 72 hr | HCT116 | rep2 |
SRR24302010 | WT | 0.1 % FBS, 72 hr | HCT116 | rep1 |
SRR24302011 | WT | 9.1 % FBS, 72 hr | HCT116 | rep3 |
SRR24302012 | WT | 9.1 % FBS, 72 hr | HCT116 | rep2 |
SRR24302013 | WT | 9.1 % FBS, 72 hr | HCT116 | rep1 |
SRR24302014 | DROSHA_KO | GFP | HCT116 | rep1 |
SRR24302015 | WT | no treatment | HCT116 | rep1 |
SRR24302016 | DROSHA_KO | DROSHA-p140 | HEK293E | rep3 |
SRR24302017 | DROSHA_KO | DROSHA-p140 | HEK293E | rep2 |
SRR24302018 | DROSHA_KO | DROSHA-p140 | HEK293E | rep1 |
SRR24302019 | DROSHA_KO | full-length DROSHA | HEK293E | rep3 |
SRR24302020 | DROSHA_KO | full-length DROSHA | HEK293E | rep2 |
SRR24302021 | DROSHA_KO | full-length DROSHA | HEK293E | rep1 |
SRR24302022 | DROSHA_KO | DROSHA-p140 | HCT116 | rep3 |
SRR24302023 | DROSHA_KO | DROSHA-p140 | HCT116 | rep2 |
SRR24302024 | DROSHA_KO | DROSHA-p140 | HCT116 | rep1 |
SRR24302025 | DROSHA_KO | full-length DROSHA | HCT116 | rep3 |
SRR24302026 | DROSHA_KO | full-length DROSHA | HCT116 | rep2 |
SRR24302027 | DROSHA_KO | full-length DROSHA | HCT116 | rep1 |
Download data
Prepare the following PBS Pro script to submit the request to download of files to the HPC cluster.
| Code Block |
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#!/bin/bash -l #PBS -N download _ENA _data #PBS -l select=1:ncpus=2:mem=8gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/023/SRR24302023/SRR24302023.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/017/SRR24302017/SRR24302017.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/019/SRR24302019/SRR24302019.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/012/SRR24302012/SRR24302012.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/026/SRR24302026/SRR24302026.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/027/SRR24302027/SRR24302027.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/013/SRR24302013/SRR24302013.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/015/SRR24302015/SRR24302015.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/021/SRR24302021/SRR24302021.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/024/SRR24302024/SRR24302024.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/010/SRR24302010/SRR24302010.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/018/SRR24302018/SRR24302018.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/022/SRR24302022/SRR24302022.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/011/SRR24302011/SRR24302011.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/009/SRR24302009/SRR24302009.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/016/SRR24302016/SRR24302016.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/020/SRR24302020/SRR24302020.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/008/SRR24302008/SRR24302008.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/025/SRR24302025/SRR24302025.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR243/014/SRR24302014/SRR24302014.fastq.gz |
...
Monitor progress of job:
| Code Block |
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qjobs |
Preparing “sample sheet” index file:
| Code Block |
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#fetch samples names
ls --color=never *.gz -1 | awk -F "." '{print $1}' > sample.names
#fetch the path to each FASTQ file
for i in `ls --color=never *.gz`; do echo $i; readlink -f $i >> sample.path ; done
#merge the sample names and FASTQ path
echo "sample,fastq_1" > samplesheet.csv
paste sample.names sample.path | awk '{print $1 "," $2}' >> samplesheet.csv
#remove intermediate files
rm sample.names sample.path |