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