coordinate of BAM and BED

Question

[yuabrahamliu]

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.

Answer 1

[Devon Ryan]

BAM files are never 1-based, they are always 0-based and samtools will never change this. What you've likely noticed is that the SAM file you see with samtools view is 1-based, since SAM uses 1-based coordinates. Regardless, bedtools is aware of the coordinates used in its supported file types and handles that properly internally.