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

Question

[kanwarjag]

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?

Answer 1

[Ashutosh Pandey]

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.

[Mathew Bunj]

Could you be little more specific.

[Ashutosh Pandey]

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

[kanwarjag]

It is a Paired end Miseq data (2X150)

[Ashutosh Pandey]

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