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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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Input files for ImRep #10

Closed PoslavskySV closed 7 years ago

PoslavskySV commented 7 years ago

Hi,

according to wiki I can't just use raw .fastq files. Instead, I need to map raw reads with some external aligner and then extract reads somehow from .bam in order to make the data suitable for ImRep. So, could you please help with the following issues:

  1. Which aligner (TopHat, STAR etc.) should I use for aligning the raw .fastq data in order to obtain .bam?
  2. When I have prepared .bam (e.g. using STAR aligner and including unmapped reads into the same .bam file with --outSAMunmapped Within option) what exact bash commands (using samtools or either) should I execute in order to produce a valid .fastq file that is suitable for ImRep?

Thanks!

smangul1 commented 7 years ago

Hi,

We would recommend running ROP pipeline, which includes the latest imrep version and will extract reads mapped to BCR and TCr genes plus unmapped reads from the bam file. We had a good experience with STAR, so i think this is a good option. Make sure to run with --outSAMunmapped Within option to include unmapped reads in the bam file.

We are planning to push new release of ROP today. We will let you know once it is available.

Some information is here:

https://github.com/smangul1/rop/wiki/Immune-profiling-by-ROP-(ImReP)

Thanks, Serghei and Igor