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