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I am using multiBamCov from bedtools to count reads in my bed file. I want to count the reads in the specified bins in my bed file such that if the read in the bam file overlap the interval more than 50%, so 51% those should be counted. I am using this command:

multiBamCov -f 0.51  -bams A549_ENCSR000DMZ_REP1_1hit_0mis_IS_Aligned.sortedByCoord.out.bam -bed test.bed

But I get all counts as 0. What am I doing wrong here?

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  • $\begingroup$ Have you looked at those regions in IGV or IGB? Are there reads that appear to meet your criteria by eye? Do the chromosome names match between the BAM and BED files? $\endgroup$ – Devon Ryan Sep 7 '19 at 20:30
  • $\begingroup$ Hi Devon, I looked at IGV and the location has reads. Also I found this link which explains why multiBamCov does not work. groups.google.com/forum/#!topic/bedtools-discuss/hzRnjQfhyZM $\endgroup$ – user3138373 Sep 9 '19 at 15:49

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