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rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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DRS read adapters... #27

Closed nickschurch closed 6 years ago

nickschurch commented 7 years ago

Will porechop identify and trim adapters in the Nanopore reads from the new DRS protocol?

rrwick commented 7 years ago

Hi Nick,

I suspect not, though I haven't actually tried as I don't have any direct RNA reads to play with. If you have any data share (even just a small number of reads), I might be able to add the adapters in. Let me know!

Ryan

phiweger commented 6 years ago

Did you integrate the DRS adapters yet? If not, I could send you some data. Which address should I send it to?

rrwick commented 6 years ago

As I just said in issue #40, I added the DRS adapters to Porechop's development branch, but I'm still lacking a test read set, so I'm not sure if they work correctly or not. Hopefully I'll get my hands on one soon, and if it all looks good, I'll move the additions to the master branch and make a new release of Porechop.

nickschurch commented 6 years ago

This could be a good test dataset:

https://github.com/nanopore-wgs-consortium/NA12878/blob/master/RNA.md

On Wed, 10 Jan 2018 at 01:47 Ryan Wick notifications@github.com wrote:

As I just said in issue #40 https://github.com/rrwick/Porechop/issues/40, I added the DRS adapters to Porechop's development branch, but I'm still lacking a test read set, so I'm not sure if they work correctly or not. Hopefully I'll get my hands on one soon, and if it all looks good, I'll move the additions to the master branch and make a new release of Porechop.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rrwick/Porechop/issues/27#issuecomment-356473148, or mute the thread https://github.com/notifications/unsubscribe-auth/ACHCLqqsudzUKO5YewRH7aaPnw9mGiLTks5tJBazgaJpZM4O_8Oo .

rrwick commented 6 years ago

Thanks for that! I took a good look at it and discussed my results in issue #40. I'll close this issue now because it's essentially the same as #40.

Ryan