Serghei Mangul

Dear chkcole, Using Imrep we were able to profile B and T cell receptors across all GTex samples. Some of the data is available as the resource here https://smangul1.github.io/TheAIR/ We...

Hi Yiwei, You are right that STAR produces partially-mapped reads, which are potentially T or B receptor reads. I would recommend saving the bam file with both mapped and unmapped...

Hi Yiwei, Please merge PE into one file. Also to use --digGold, you need to provide original reads, not the unmapped reads. Please let me know how it goes. If...

as we can offer this option. Maybe we can find more CDR3 reads? Also, we can concatenate corresponding V and J genes and map. What do you think?

/u/home/s/serghei/project/imrep_gtex/validation/BCR-Seq/imrep/SRR5248346.cdr3 the file containing that line

Thanks! Would you mind sharing the modified script with us!

Thanks! I think the problem was with perl path Looks like it was fixed by running export PERL5LIB="/PHShome/sv188/anaconda2/envs/polysolver/lib/perl5/5.22.0/" maybe you can add this to conda build S

Wow! It works! I was able to run on our WXS data! Thanks a lot for releasing this conda package! Do you think you can update it with export PERL5LIB="/PHShome/sv188/anaconda2/envs/polysolver/lib/perl5/5.22.0/"...

Great! I think conda and docker containers should be a must for any published tool. So we don't need t do this work :)