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?