cutadapt extra trimming

[crisalves80]

Hi @MikeAxtell ,
The auto trimming will look for adapters, but what about kits (NextFlex) that add 4Ns on both 3' and 5' end? Usually, I trim those extra bases after the adapter. Is there a way to add this option to the package, so we don't need to do it before running ShortStack?

Also, there is no phasing score anymore? Is there a way to access this information? I need this info for my analysis.

Thanks

[MikeAxtell]

• autotrim: Thanks for the heads up. I haven't seen data like that before. It's good to know about it. I can modify the auto trim methods to allow a user to specify a certain number of leading N's before the fixed adapter. Will do that for the next release.
• phasing: This was a deliberate decision. I have lost confidence in genome-wide phasing scores. Or at least, I have lost confidence in my ability to reliably score them. See #117

[crisalves80]

Thanks @MikeAxtell !

[MikeAxtell]

@crisalves80 I am starting to work on this. I would like some test data for development. Can you provide accession numbers (SRA, etc.) to public sRNA-seq datasets (that correspond to publicly available genome assemblies) that have 5' and/or 3' Ns? I don't want to release the code without testing it on real data; in my group we only have used and generated more traditional libraries where nt 1 is the 1st sRNA nt, and the adapter begins immediately after the last sRNA nt.

[crisalves80]

@MikeAxtell I don't know any public dataset. We haven't published data using the NextFlex kit in our lab yet. I might be able to send you some unpublished datasets....

[MikeAxtell]

@crisalves80 sure that would be fine. I will keep them confidential. Get in touch with me by email to set up.

[MikeAxtell]

Closing due to inactivity. I am still open to adding some support for unusual adapter trimming, but do need test data first.