Question: STAR output processing
0
gravatar for kintany
3.8 years ago by
kintany10
kintany10 wrote:

Hi all,

I'm running STAR to align RNA-seq reads separately to paternal and maternal genomes for subsequent analysis of allele-specific expression with GATK tools. So as an output I have two BAM files.

I want to keep reads aligned uniquely to only one genome and in cases where reads mapped uniquely to both genomes, use the alignment with the higher alignment quality.

Are there any existing tools for it? I can write a script doing this but I would prefer to use existing tool if there is one.

Thank you!

rna-seq star ase • 2.1k views
ADD COMMENTlink written 3.8 years ago by kintany10

BBMap/BBSplit from the BBTools suite might be able to do this.

ADD REPLYlink written 3.8 years ago by Sinji3.0k

So you have two separate reference genomes? While BBSplit would certainly be an option (as indicated by @Sinji) multi-mapping is going to make this tricky. What exactly are you trying to do?

Will go ahead and tag : Brian Bushnell

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by genomax92k

Yes, I'm mapping to two separate genomes. Then I want to use ASEReadCounter from GATK for ASE statistics. It requires BAM file as input so I need to find a way to create this file from two BAM files that I have now

ADD REPLYlink written 3.8 years ago by kintany10

I don't think that strategy will work. ASEReadCounter uses a single BAM. The strand is based on the alleles of the reads ("tool calculates allele counts at a set of positions"). Even if you could use two BAMs or merge them as one, the paternal and maternal reads would not align to the same position.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by igor11k

one set of fastqs mapped to two REF genome = two BAM, isn't it ?

ADD REPLYlink written 3.8 years ago by Pierre Lindenbaum131k

yes, that's what I'm saying

ADD REPLYlink written 3.8 years ago by kintany10
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