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aperdomos 01-24-2012 07:41 AM

How to subtract specific DNA sequences from *mpileup* files (programs and scripts)
Hello everyone,

I have around 100 mpileup files from different species. These files have some specific DNA regions that are of my interest, since they include some genes that I want to compare. According to the pileup format generated with Samtools, these files have these columns:
chr pos ref coverage

Therefore, using these pileup files I want to specifics parts of the sequences, but keeping the information about position, and coverage. For example: DNA sequence from Samples A, B, C, etc from 33566 to 38000; 56000 to 59000; 110000 to 112500 and that presented a coverage of more than 10.

Consequently, I want to know if there is some specific programs that help to perform this, or if it is necessary to design a specific script. Does anyone have any script already designed that can be useful to subtract this info?

Many thanks,


swbarnes2 01-24-2012 09:34 AM

Starting from pileups? There isn't going to be much software written that's designed to take pileups as input. You have lots more options if you had .bams. SAMtools or BEDTools can both take .bam files and .bed files with your regions, and filter the .bam to only contain reads from those region. BEDTools also has some programs that will calculate coverage for you. So go back to the .bams if you still have them. Otherwise, I think a simple script can do what you want.

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