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  • featureCounts vs bedtools multicov

    --hello,

    i try to compare the programs featureCounts and bedtools multicov to count reads into a little bam file.
    So i use those commands:

    featureCounts -F SAF -p -Q 27 -a myannot.txt -o results.txt 17PT1.bam

    with myannot.txt with one single line and formated as:

    47 TR34|c0_g1_i1 0 387 -

    For bedtools i use:

    bedtools multicov -D -q 27 -p -bams 17PT1.bam -bed myannot.bed

    with myannot.bed with one single line and formated as:

    TR34|c0_g1_i1 0 387

    you can download the bam file from this link:


    with featureCounts i obtain 32 results
    and with bedtools i obtain 54 results.

    I don't understand why this difference in counting ?

    thank you --

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