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Which Parameter To Select -P (Pe Mode) In Shrimp2

Shrimp2 has four options for PE ---"opp-in", "opp-out", "col-fw" and "col-bw". These correspond to: opposing strands, inwards; opposing strands, outwards; colinear, second is forward; colinear, second is backward

While aligning reads to bacteria/ virus genome which mode should be selected from above options?

paired bacteria
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updated by Ashutosh Pandey Ashutosh Pandey • written by kanwarjag kanwarjag

1 answer

Hi, The answer to this question has nothing to do with which kind of genome you want to align you reads to. It depends on what type of library was generated before the reads were sequenced. I assume you are using some public data. I would try to find some metadata about the sample. For eg. is it paired end OR mate pair library OR fragment library? Then read about different types of NGS libraries on internet.

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written by Ashutosh Pandey Ashutosh Pandey

If it is Miseq paired end data then "opp-in" is the mode to be used with SHRIMP2.

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written by Ashutosh Pandey Ashutosh Pandey

It is a Paired end Miseq data (2X150)

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written by kanwarjag kanwarjag

Same as above. "Opp-in" mode should be used to align Paired end reads from Miseq/Hiseq data.

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written by Ashutosh Pandey Ashutosh Pandey

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