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Old 06-14-2016, 01:59 PM   #1
rags_brown
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Location: providence

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Default RNA- Seq annotate only multimapping reads.

Hi,

I am working with 50bp single end reads to perform differential gene expression analysis. I use STAR to map the reads and I figured out a way to only filter those reads that were mapping at multiple loci. Surprisingly this was almost 20% of my total reads and hence wanted to identify which genes/transcripts or part of the genome these reads overlap with. Is there a way to annotate these multi mapping reads?

I cannot use HTSeq as it will categorize all my reads as multi mappers. I tried converting my sam file to bed and tried to use bedmap and that did not work either.

Any reasonable explanation and tip will be helpful.

Thanks,
Raghavee
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annotation file, multi-mapping, rna sequencing, star aligner

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