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Old 03-12-2013, 02:06 AM   #1
Location: India

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Default How to extract unmapped reference sequence from BAM/SAM file.?

How to extract unmapped region from reference sequence from SAM/BAM file.?
Pinal is offline   Reply With Quote
Old 03-12-2013, 05:55 AM   #2
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you can use the function coverageBed included in the bedtools suite and then, (for example using the Rpackage Rsamtools), it is really easy to select the uncovered region of your reference and extract the corresponding sequence...
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Old 03-06-2014, 12:40 PM   #3
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Does anybody know any other way to extract unmapped regions of the reference sequence from a BAM/SAM/ACE file??
Biologist and Bioinformatics at Universidad of Barcelona
Jose F. Sanchez
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