[shi]

Hi every one,
After I converted bowtie sam files to the bam files, I have no idea which bam should be used to cound reads, because there are tow bam files--- .bam file and .bam.sorted file. Is there any one who can do me a favor?

Thanks a lot!!

Richard

The featureCounts program included in Subread package can count reads for both sorted and unsorted BAM files. If your BAM file contains paired-end reads and they were sorted by coordinates, you can use '-S' flag to instruct featureCounts to re-sort reads by their names and then perform read counting.