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Old 01-24-2012, 07:41 AM   #1
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Location: Sydney

Join Date: Jan 2012
Posts: 8
Default 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,

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