Question: coordinate of BAM and BED
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yuabrahamliu • 60 wrote:
Hi all,
I want to use bedtools multicov to count the RNAseq reads in specific bed file intervals (containing all the intron intervals of mm10 genome downloaded from UCSC). However, I noted that the BED file coordinate is 0-based, while the BAM file used by bedtools multicov was sorted by samtools and its coordinate was 1-based. So, do I need to transform the coordinate of the BAM file from 1-based to 0-based before run the bedtools multicov command? Thank you.
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modified 3.2 years ago
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Devon Ryan ♦ 98k
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written
3.2 years ago by
yuabrahamliu • 60
