ROP analysis of multiple sample modified by Serghei Mangul

Serghei Mangul — Sun, 26 Jun 2016 07:26:24 -0000

--- v1
+++ v2
@@ -18,3 +18,8 @@

 #####
 while read line ; do echo "python /u/home/s/serghei/code2/rop/rop.py --qsubArray /u/home/s/serghei/collab/bloodMicrobiome_Oct20/data/replicationRNASeq/data/unmapped/unmapped_${line}.fastq $PWD/${line}/">run_${line}.sh;done<../samples.txt
+
+
+1) ls *sh | awk '{i+=1;print "if [ $1 == "i" ];then ./"$1" ;fi"}' > myFunc.sh
+2) wc -l myFunc.sh
+3) qsub -cwd -V -N tophat2 -l h_data=8G,express,time=10:00:00 -t 1-x:1 myFuncFastWrapper.sh

ROP analysis of multiple sample modified by Serghei Mangul

Serghei Mangul — Sun, 26 Jun 2016 07:26:24 -0000

Run ROP for all the samples at once :

while read line; do ; python /u/home/s/serghei/code2/rop/rop.py --qsubArray --skipQC /u/home/b/brigitta/scratch/gtex/data/${line}.fasta $PWD/${line}; done<../samples_26.txt

ls /CR//runsh | awk '{i+=1;print "if [ $1 == "i" ];then ./"$1" ;fi"}' > myFunc.sh

cp /u/home/s/serghei/code2/rop/myFuncFastWrapper.sh ./
chmod 755 myFunc.sh

chmod 755 /CR//sh
wc -l
qsub -cwd -V -N rop -l h_data=16G,time=24:00:00 -t 1-2002:1 myFuncFastWrapper.sh

while read line; do ; python /u/home/s/serghei/code2/rop/rop.py --qsub --skipQC /u/home/b/brigitta/scratch/africa/data/${line}.fasta $PWD/${line}; done<../samples_26.txt

while read line ; do echo "python /u/home/s/serghei/code2/rop/rop.py --qsubArray /u/home/s/serghei/collab/bloodMicrobiome_Oct20/data/replicationRNASeq/data/unmapped/unmapped_${line}.fastq $PWD/${line}/">run_${line}.sh;done<../samples.txt

Recent changes to ROP analysis of multiple sample

ROP analysis of multiple sample modified by Serghei Mangul

ROP analysis of multiple sample modified by Serghei Mangul