/cmd

Miscellaneous scripts for hoffman2

Primary LanguagePython

install DESeq2 on hoffman2

Notice : http instead of http

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Subsample BAM file. In house script

python subsampleBam.py old.bam new.bam 0.5

Transfer friles from/to Google Drive

gdrive download --recursive 0B6t4h9kX59LaTXVKeE9GSEl2WEk

DE - to be moved to DE dir

Rename files

for f in *; do new=$(echo $f | sed 's/mapped_//' | sed 's/-V//'); mv $f $new;done

Connect cluster to github

  • On the culster

https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/

  • On the git hub page

https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/

misc-scripts-hoffman2

Miscellaneous scripts for hoffman2

Copy to GDrive vs cmd

Am example how to run copy2gDrive.sh

~/code2/misc-scripts-hoffman2/copy2gDrive.sh *sam 0Bx1fyWeQo3cOWk8ybjNkd1VPMTg sam

sam to bam for multiple files via qsub

while read line; do echo ". /u/local/Modules/default/init/modules.sh">run_${line}.sh; echo "module load samtools">>run_${line}.sh; echo "samtools view -bS ${line}.sam | samtools sort - ${line}.bam">>run_${line}.sh;done<sample.xt

Run tophat2 hoffman2 : split by 1M and run

  • Example
run.sh :
/u/home/s/serghei/code/cmd/runTophat_PE_FASTQ.GZ.sh  /u/home/k/kwesel/scratch/new_fastq_PE/data/ $PWD/tophat/ /u/home/s/serghei/project/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome "-G /u/home/s/serghei/project/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"


qsub -cwd -V -N prepare -l h_data=8G,time=5:00:00 run.sh