--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 --
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 --