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How many basepairs are genes padded by in WES?

When working with whole exome sequencing data, how many basepairs should I expect as padding for a given gene: 0, 100, 1000? For example, would the upstream transcription factor binding site for each gene be included?

ngs sequencing wes exome
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updated by Prash • Prash • written by LayneSadler LayneSadler

1 answer

A great question, Kermit. IMHO, it all depends on the exome capture and selection chemistry. For example, the Agilent sureselect V8 plus NCV plus 5' UTR has less bias and could pad more bases.

Are you asked for an option while running a pipeline?

Prash

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written by Prash • Prash

Ok Kermit. Pl ask your service provider about the chemistry. From BAM and sorted, you could as well but the alignment with reference matters as well.

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written by Prash • Prash

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