ROP analysis of multiple samples

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Here we explain how to compare the immune and microbiome profiles across multiple sample corresponding to different phenotypes or disease groups.

while read line ; do echo "python ~/collab/code/rop/rop.py $PWD/unmaaped/${line}.fastq $PWD//rop/${line} --qsubArray">run_${line}.sh;done<sample.txt

The proposed command will create individual .sh file for each sample. To run all .sh via qsub, use the following commands

ls run*sh | awk '{i+=1;print "qsub -cwd -V -N ropBrain"i" -l h_data=16G,time=10:00:00 "$1}' > all.sh

chmod 755 all.sh

nohup ./all.sh &

In case you have filtered fasta files (after step 1-2 of ROP) and you are planning to do microbiome profiling only, use this command:

while read line ; do python ~/collab/code/rop/rop.py --skipPreliminary --microbiome  --qsub $PWD/afterQC/${line}.fasta $PWD//rop2/${line};done<samples.txt

If the number of samples is larger then the number of jobs allowed on the cluster use --qsubArray.

while read line ; do python /u/home/s/serghei//collab/code/rop/rop.py --skipPreliminary --microbiome  --qsubArray $PWD/data/${line}.fasta $PWD//rop/${line};done<sample.txt

This command should finish fast. Next you need to generate myFunc.sh

ls */microbiomeProfile/*/run* | awk '{i+=1;print "if [ $1 == "i" ];then ./"$1" ;fi"}' > myFunc.sh
chmod 755 */microbiomeProfile/*/run*

Next count how many jobs you have:

wc -l myFunc.sh

Copy the myFuncFastWrapper.sh from ROP directory

cp <dir>/rop/source/myFuncFastWrapper.sh ./

Now you are ready to submit job array:

qsub -cwd -V -N rop -l h_data=16G,express,time=24:00:00 -t 1-1573:1 myFuncFastWrapper.sh

This is the message you expect see

Your job-array 30090.1-1573:1 ("rop") has been submitted

Congratulations!!! Now you are running 1573 jobs!!!

After you prepared the filtered fasta file (after step1-2) you can run a targeted analysis to profile B cell and T cell receptors as follows:

ls */antibodyProfile/*/*/run* | awk '{i+=1;print "if [ $1 == "i" ];then ./"$1" ;fi"}' > myFunc.sh
chmod 755 */antibodyProfile/*/*/run*