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  • #16
    Originally posted by wmseq View Post
    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.

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