FeatureCounts output to SAM like htseq-counts?

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courtney.stairs • 0

@courtneystairs-13043

Last seen 5.7 years ago

Hi there,

I have been using featureCounts for quite some time now and I really like it. However, I have come across a workflow for deconvoluting multimapping of RNAseq reads to multiple genes (RNAfreak) that requires the output of htseq-counts since it gives a read summaries (i.e., the fate of each read) in a SAM file. In particular, I am interested in multimapping information that is provided in the htseq-counts SAM file output defined in one of the columns ("XF:Z:....")

Is it possible to have the read information from featurecounts output to a SAM file?

Thanks a lot!

Courtney

example of htseq-counts SAM file output where GENE_id will be the gene name if it was uniquely mapped or "__ambiguous[GENE_id1+GENE_id2...]"

READname    99    KI546164    34680    255    1S125M    =    34701    147    READseq READqual      NH:i:1    HI:i:1    AS:i:249    nM:i:0    XF:Z:GENE_id

featurecounts SAM htseqcounts • 2.6k views

ADD COMMENT • link updated 16 months ago by Yang Liao ▴ 450 • written 7.5 years ago by courtney.stairs • 0

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This is something we are currently working on. Will try to add this feature soon.

ADD REPLY • link 7.5 years ago Wei Shi ★ 3.6k

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Great! Thank you! I'll keep an eye out!

ADD REPLY • link 7.5 years ago courtney.stairs • 0

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Hi,

I'd also like to use the same workflow and wanted to ask if this feature has been added already.

Kind regards

Lara

ADD REPLY • link 17 months ago lara.dreide • 0

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This parameter of featureCounts gives per-read assignment results in the SAM format:

reportReads="SAM"

Alternatively, you can give it "BAM" to generate per-read assignment results in the BAM format.