Does imrep work with BAM files from HISAT2 aligner?

mandricigor / imrep

ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.

https://mandricigor.github.io/imrep/

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Does imrep work with BAM files from HISAT2 aligner? #33

Closed ooondrej closed 6 years ago

ooondrej commented 6 years ago

Hi, I trying to apply imrep on my bulk paired-end RNA seq data aligned with HISAT2 to hg38 (ucsc). Does the BAM have to come from STAR? I am having this error message ValueError: invalid reference 14which is most likely caused by alignment to a different reference than imrep is using? What reference is imrep using?

Many thanks for your help!

smangul1 commented 6 years ago

Hi,

I expect the build have chromosome names as : chr1, chr2, etc

If this is true you to use this option : --chrFormat2

Alos please make sure to use --hg38 option

Thanks, Serghei

ooondrej commented 6 years ago

Hi Serghei, many thanks for your advice - it is working brilliantly now! BW, Ondrej

smangul1 commented 6 years ago

Great! I am closing the issue then! S