...
Create a working directory on scratch3 scratch and change into the newly-created directory. For example, for user abc123, the working directory will be
| Code Block |
|---|
mkdir /n/scratch3scratch/users/a/abc123/chipSeq cd /n/scratch3scratch/users/a/abc123/chipSeq |
Build a barcode file for demultiplexing library:
...
| Code Block |
|---|
runAsPipeline "fastxBowtie2.sh -r hg38" "sbatch -p short --mem 6G -t 2:0:0 -n 1" noTmp #Or if you want to use your own bowtie2 index: runAsPipeline "fastxBowtie2.sh -b /n/scratch3scratch/users/a/abc123/index/hg38GenomeWithChr11Report" "sbatch -p short --mem 6G -t 2:0:0 -n 1" noTmp # this is a test run |
...
| Code Block |
|---|
runAsPipeline "fastxBowtie2.sh -r hg38" "sbatch -p short --mem 6G -t 2:0:0 -n 1" noTmp run 2>&1 | tee output.log #Or if you want to use your own bowtie2 index: runAsPipeline "fastxBowtie2.sh -b /n/scratch3scratch/users/a/abc123/index/hg38GenomeWithChr11Report" "sbatch -p short --mem 6G -t 2:0:0 -n 1" noTmp run 2>&1 | tee output.log # notice here 'run 2>&1 | tee output.log' is added to the command |
...