featureCounts vs bedtools multicov

[mslider]

--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:

http://vital-it.ch/prd/lmanchon/17PT1.zip

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

I don't understand why this difference in counting ?

thank you --