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Old 03-08-2014, 11:18 AM   #1
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Location: singapore

Join Date: Feb 2014
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Post get sequence context from a reference genome

hi, everyone.
If I have a tsv file of somatic mutation profile that contains information of:
1. mutation information (for example, a mutation from T -> C)
2. its mutation position from a reference genome (for example, chrX:0003)

Question: how to get a profile of 3-based mutational sequences that have the mutational base and their 5' and 3' context? ( for example ATC -> ACC, the ACC sequence is what we need, and the ATC is its corresponding reference genome sequence). What tool or method should I use to generate this kind of profile? As a beginner, I have no idea about how to solve this problem.

Hope anyone could help me, thanks!
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mutation, reference genome, sequence

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