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ababaian / serratus

Ultra-deep search for novel viruses
http://serratus.io
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Additional PFAM alignments #206

Closed rcedgar closed 3 years ago

rcedgar commented 3 years ago

  1. I need PFAM alignments for these fragments for OTU construction: cov5_fragment_final.id99.fa

  2. I also need PFAM alignments for the missing GB complete genomes due to the VADR bug (#203).

@taltman @rchikhi would it be possible to get these done more quickly & easily by running PFAM on the ORFs instead of waiting for a VADR fix? You could use any cli ORF-finder, e.g. EMBOSS getorf and run PFAM on those.

taltman commented 3 years ago

Sure, I can run then this weekend.

On July 17, 2020 1:11:18 PM PDT, Robert Edgar notifications@github.com wrote:

  1. I need PFAM alignments for these fragments for OTU construction: cov5_fragment_final.id99.fa

  2. I also need PFAM alignments for the missing GB complete genomes due to the VADR bug (#203).

@taltman @rchikhi would it be possible to get these done more quickly & easily by running PFAM on the ORFs instead of waiting for a VADR fix? You could use any cli ORF-finder, e.g. EMBOSS getorf and run PFAM on those.

-- You are receiving this because you were assigned. Reply to this email directly or view it on GitHub: https://github.com/ababaian/serratus/issues/206

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rchikhi commented 3 years ago

I'm stealing point 1. from your plate @taltman !

rchikhi commented 3 years ago

Results for cov5_fragment_final.id99 are coming to https://s3.console.aws.amazon.com/s3/buckets/serratus-public/seq/cov5/annotations/?region=us-east-1&tab=overview and will be completed in ~30mins

taltman commented 3 years ago

@rchikhi Can you briefly describe how you did this? I don't recommend most ORF callers for this application due to frame shifts. FragGeneScan is the only one that I am aware of that handles this.

rchikhi commented 3 years ago

I ran Darth :) on each of these fragments.

rcedgar commented 3 years ago

Any generic ORF caller is fine, there are no frameshifts within the PFAM domains. E.g. I use getorf in serratax. Note that PFAM domains are shorter than the full-length gene / ORF / CDS / cleaved product (any of these).

rcedgar commented 3 years ago

Closed, issue superseded by #211.