extract VDJ recombinations

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Serghei Mangul edited this page May 15, 2016 · 2 revisions

Here we explain hot to extract reads spanning VDJ recombinations

python ~/code2/rop/source/iprofile/extract_VDJ.py unmapped_108318A_IGL_igblast.csv $PWD/VJ/ IGL 1e-05

If case you have many samples, which are saved in a directory

for f in IGK/* ; do python ~/code2/rop/source/iprofile/extract_VDJ.py $f $PWD/VJ/ IGL 1e-05;done

Don’t let your unmapped reads go to waste