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Question: coordinate of BAM and BED
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gravatar for yuabrahamliu
2.7 years ago by
yuabrahamliu • 40
yuabrahamliu • 40 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.
rna-seq alignment genome • 1.3k views
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modified 2.7 years ago by Devon Ryan ♦ 95k • written 2.7 years ago by yuabrahamliu • 40
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gravatar for Devon Ryan
2.7 years ago by
Devon Ryan ♦ 95k
Freiburg, Germany
Devon Ryan ♦ 95k wrote:

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.
ADD COMMENT • link written 2.7 years ago by Devon Ryan ♦ 95k
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