I use tophat do the mapping and get .bam file. I try to use featureCount. Here are some question about my data:
1.I use pair-end reads also single-end reads in tophat, so the mapping result contain both.Which arguments I should use?
2.my annotation file is gff3 but I check the parameter in featureCount such as "-g"(GTF.attrType),I find almost everyone use -g gene_id. And gff3 use "ID=" and "parent=". I can't get any result with my gff3 file so I convert it to gtf. Now I get read count, is it reliable? or how to deal with gff3?
here is my command usage:
featureCounts -a my.gtf -t exon -g gene_id -o counts.txt accepted_hits.bam