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.
Question: coordinate of BAM and BED
0
yuabrahamliu • 60 wrote:
ADD COMMENT
• link
•
modified 3.2 years ago
by
Devon Ryan ♦ 98k
•
written
3.2 years ago by
yuabrahamliu • 60
1
Devon Ryan ♦ 98k 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.
Please log in to add an answer.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2010 users visited in the last hour