Compare two bam files.

[fabrice]

I have used two different map software to map my pair-end reads.

I want to how many reads are reported as mapped by these two map software and how many reads only reported in one map software.

Is there some easy ways to do this?

Thank you

[upendra_35]

Is your aim is to compare the % of mapped reads? Then you should convert this to sam file. There is a related query at this thread: http://seqanswers.com/forums/showthr...hlight=upendra.

Good luck!

[fabrice]

Yes. I want to compare how many mapped reads are overlap in two method.

Thanks

Is your aim is to compare the % of mapped reads? Then you should convert this to sam file. There is a related query at this thread: http://seqanswers.com/forums/showthr...hlight=upendra.

Good luck!

[Dario1984]

Do you use R ? It is easy to do. You need the packages Rsamtools and GenomicRanges installed.

Rsamtools has a function called readBamGappedAlignments. Use it on each file to read the BAM file into memory.

Then, use the findOverlaps function in the package GenomicRanges to find which reads in one sample overlap with reads in the other.

You don't need to create unnecessary SAM files on your hard drive this way.

[cedance]

you can use "samtools view" to output a *.bam file on the go.
however using R + IRanges seems to be the best option for me. Else you'll have to find modules on interval trees (if any) and implement in perl. But why reinvent the wheel if the purpose here is to get the job done.