[BioC] HT-Seq count and GTF

Simon Anders anders at embl.de
Wed Jul 17 17:30:02 CEST 2013


Hi Jose

not sure what is going on.

The best might be to take one of these reads (find the read ID in IGV, 
then grep for it in the SAM file) and first check whether it might be 
multiply aligned ("NH" field). Then, make a mini SAM file with only this 
read and feed it to hseq-count, with the "--samout" option, to see what 
the script does with it.

   Simon



More information about the Bioconductor mailing list