...
(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.
...
Monitor progress of job:
| Code Block |
|---|
qjobs |
Preparing “sample sheet” index file:
| Code Block |
|---|
#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 |