search

smangul1 / rop

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.
https://github.com/smangul1/rop/wiki
GNU General Public License v3.0
35 stars 14 forks source link

Enable circrna and bacteria steps #135

Closed kahsieh closed 1 year ago

kahsieh commented 6 years ago

The circrna and bacteria databases have been missing since v1.0.8. This should be addressed.

smangul1 commented 6 years ago

I will am building bacteria database. As soon as this is done, we can make bacteria step optional. We will also make NCL step optional. I think it should be ready, just make sure to test it. It is taking a lot of time, so I suggest to make it optional. Serghei

kahsieh commented 6 years ago

The metaphlan database also appears to be broken now, so I'm disabling that step for now.

InesdeSantiago commented 6 years ago

Is metphlan dbase still broken? can you enable it now?

smangul1 commented 6 years ago

Sorry for the delay! We are working on this now and expect the update by the end of the week!

kahsieh commented 6 years ago

Metaphlan has been re-enabled.

InesdeSantiago commented 6 years ago

Great! Thank you !

On Wed, 28 Nov 2018 at 19:19, Kevin Hsieh notifications@github.com wrote:

Metaphlan has been re-enabled.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/smangul1/rop/issues/135#issuecomment-442570989, or mute the thread https://github.com/notifications/unsubscribe-auth/AGp8R2tejVyWRv72cqucJUA8bZaizPNeks5uzuHdgaJpZM4TCuLH .

david-a-siegel commented 3 years ago

Hi, is there any update on the bacterial database, or an old database we can use in the meantime?

kahsieh commented 3 years ago

Unfortunately, I think it's unlikely that we'll be able to bring back circrna/bacteria support.

david-a-siegel commented 3 years ago

Is there something wrong with the original one? Do you have a reference file we could use and call bwa-mem ourselves?

kahsieh commented 3 years ago

Could you try asking @smangul1? (See http://www.sergheimangul.com/ if he doesn't respond here)