SEA-PHAGES | Question about notes template

Link to this post \| posted 08 Oct, 2021 20:05
afreise	Hi everyone, Our former primary SEA-PHAGES faculty member, Jordan Parker, was an expedited submitter and had been doing things somewhat differently than the general SEA-PHAGES requirements. For example, she (and I) have been asking students to take notes using a customized template in the PECAAN "Notes" box. Jordan has since left UCLA and I am now the primary faculty for SEA-PHAGES at UCLA. Now that Jordan has left UCLA, I need to return to the standard SEA-PHAGES requirements for recording annotations since I am not an expedited submitter. Since we have been completing our annotations in PECAAN since I started teaching the course, I want to make sure I'm doing things correctly going forward. The PECAAN output actually does follow the DNA Master notes requirements exactly - so do I need to make edits to our template and/or have students fill things out differently as we complete our primary annotations in PECAAN? Or is the standardize PECAAN output sufficient? I have attached the output from PECAAN for PumpkinSpice so you can see the template we are using, if that is useful. Hopefully this is acceptable for PumpkinSpice, at least, since it was a huge genome and those students have since graduated! Thank you in advance for your guidance! 652Kb

Link to this post | posted 08 Oct, 2021 20:05

Hi everyone,

Our former primary SEA-PHAGES faculty member, Jordan Parker, was an expedited submitter and had been doing things somewhat differently than the general SEA-PHAGES requirements. For example, she (and I) have been asking students to take notes using a customized template in the PECAAN "Notes" box. Jordan has since left UCLA and I am now the primary faculty for SEA-PHAGES at UCLA.

Now that Jordan has left UCLA, I need to return to the standard SEA-PHAGES requirements for recording annotations since I am not an expedited submitter. Since we have been completing our annotations in PECAAN since I started teaching the course, I want to make sure I'm doing things correctly going forward.

The PECAAN output actually does follow the DNA Master notes requirements exactly - so do I need to make edits to our template and/or have students fill things out differently as we complete our primary annotations in PECAAN? Or is the standardize PECAAN output sufficient?

I have attached the output from PECAAN for PumpkinSpice so you can see the template we are using, if that is useful.

Hopefully this is acceptable for PumpkinSpice, at least, since it was a huge genome and those students have since graduated! smile

Thank you in advance for your guidance!

Link to this post \| posted 14 Oct, 2021 19:41
dwilliams	Hi Amanda, I can't speak for everyone and have only briefly looked at the template, but this seems reasonable. If I were doing QC on PumpkinSpice, I would use your PECAAN Notes and verify it against the minimal file to make sure things are consistent. My hunch is that if you used PECAAN to annotate and keep student's work in one location, then used the PECAAN output to generate your DNAMaster complete notes and minimal file, then you should be good to go.

Link to this post | posted 14 Oct, 2021 19:41

dwilliams

Hi Amanda,
I can't speak for everyone and have only briefly looked at the template, but this seems reasonable. If I were doing QC on PumpkinSpice, I would use your PECAAN Notes and verify it against the minimal file to make sure things are consistent. My hunch is that if you used PECAAN to annotate and keep student's work in one location, then used the PECAAN output to generate your DNAMaster complete notes and minimal file, then you should be good to go.

Link to this post \| posted 14 Oct, 2021 20:12
debbie	Amanda, HI! Sorry for the delay in my response too! Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output. Use the cover sheet to describe what you have done and all should work out. debbie

Link to this post \| posted 15 Oct, 2021 01:24
afreise	Thank you both very much!

Link to this post \| posted 12 Mar, 2022 02:15
Schaudhary	debbie Amanda, HI! Sorry for the delay in my response too! Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output. Use the cover sheet to describe what you have done and all should work out. debbie Hello Debbie, I have a question, by PECAAN output do we mean the notes part as when we do the output the synteny notes written separately do not show up. Can we add it separately to the output notes. We are exporting the new SEA Format in PECAAN.

Link to this post | posted 12 Mar, 2022 02:15

Schaudhary

debbie
Amanda,
HI! Sorry for the delay in my response too!
Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output.
Use the cover sheet to describe what you have done and all should work out.
debbie

Hello Debbie,
I have a question, by PECAAN output do we mean the notes part as when we do the output the synteny notes written separately do not show up. Can we add it separately to the output notes. We are exporting the new SEA Format in PECAAN.

Link to this post \| posted 12 Mar, 2022 02:15
Schaudhary	debbie Amanda, HI! Sorry for the delay in my response too! Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output. Use the cover sheet to describe what you have done and all should work out. debbie Hello Debbie, I have a question, by PECAAN output do we mean the notes part as when we do the output the synteny notes written separately do not show up. Can we add it separately to the output notes? We are exporting the new SEA Format in PECAAN. Edited 12 Mar, 2022 02:16

Link to this post | posted 12 Mar, 2022 02:15

Schaudhary

debbie
Amanda,
HI! Sorry for the delay in my response too!
Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output.
Use the cover sheet to describe what you have done and all should work out.
debbie

Edited 12 Mar, 2022 02:16

Link to this post \| posted 15 Mar, 2022 13:16
debbie	Shima, What you need to provide is one best explanation for each gene call. Since i don't use PECAAN this way, I can't answer your question. You are correct, Claire set up PECAAN so there is an output that works. But whatever you pick, be sure to identify the problem areas and the thinking process. debbie

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