How to get the number of reads for a set of coordinates from a bam file.
I have Whole exome data and aligned them to the genome, so I also have bam files. I also have the corresponding chromosome coordinates for which I need to find the number of reads. So, the question is that how can I count the number of reads that map to each coordinate separately in the genome. in other word, I want to count the number of reads that map to the list of coordinates which I have. do you guys know how to do that? Thanks in advance
• 1,855 views
•
link
updated
by
ATpoint
•
written
by
hins.2026 •
•
written
by
hins.2026 •
1 answer
Please use the search function and google, this has been asked dozens of times, e.g:
To Calculate The Exact Total Number Of Mapped Reads In Exome Regions
Log in to answer this question.
More posts like this
-
Issues adding GTF track to split genome on IGV
written by Daisy •
-
Convert variant coordinates from one genome build to the other
written by Gene_MMP8
-
Counting reads starting at a coordinate in bam file
written by aboyd003 •
-
Count the number of reads for multiple genomic locations on different (not all) chromosomes
written by vkgaur25 •
-
How to count reads mapped to multiple loci?
written by Javad
-
counting the reads mapped only to the coding sequence
written by alirezamomeni707 •
-
counting the reads mapped to specific coordinate in the genome
written by alirezamomeni707 •
-
DIAMOND BLAST less queries aligned than reported alignment
written by dazhudou1122
-
From aligened sliced and filtered bam to single sequence in fasts format
written by rus2dil •
-
Bitwise Flag Samtools
written by rob234king
Using Python and the pysam lib you can do
To get all reads mapping at coordinate of the chosen chromosome.
or using samtools you convert it in sam and then extract the corresponding line with awk. Otherwise I'm sure tools like samtools, BEDOPS or Subread package have command dedicated for that purpose. Have a look here: Extract Reads From A Bam File That Fall Within A Given Region