Entering edit mode
2.7 years ago
askif4
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20
I have two BAM files which are the output of alignments from two different references.
I want to compare two BAM files with some criteria in order to check the difference between the two references.
What is the appropriate way to compare the two alignments(references)?
(Tool suggestions, etc..)
Just to clarify, you aligned the same set of reads to two different reference genomes?
What comparisons do you want to make? What do you want to know about the references? Maybe something like number of reads mapped? Mapping quality?
same set of reads to two different reference genomes -> yes
number of reads mapped? Mapping quality? -> yes plus unmapped reads, depth distribution, or any other known parameters for assessing BAM files.
A good place to start is the flagstat tool from samtools You can access other data with bash/python/perl. You'll need to know what you are looking for