Question: FeatureCounts output to SAM like htseq-counts?
gravatar for courtney.stairs
2.6 years ago by
courtney.stairs0 wrote:

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!


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 • 916 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by courtney.stairs0

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

ADD REPLYlink written 2.6 years ago by Wei Shi3.2k

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


ADD REPLYlink written 2.6 years ago by courtney.stairs0
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