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
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