plan for ncRNAs

[Antonialock]

We have a lot of ncRNAs in the features file and we are about to get more from Jurg.

Some are 'known' (tRNAs, snoRNAs, lncRNAs with a demonstrated regulatory function etc), some are unknown (could have a function or could be transcriptional noise?)

what to do?

I am guessing we want to keep anything with a demonstrated function in the features file?

For uncharacterised ncRNAs:

1. break out all unknown ncRNAs into one separate track?
2. break out all unknown ncRNAs into study specific tracks?

anything else to think of?

[ValWood]

• [ ] Need to create a contig file of ncRNA for each dataset.
• [ ] Ask Kim @kimrutherford about this for track hosting
• [ ] For the EMBL submission, I will merge the collection of files (tracks) into the master

[ValWood]

@bahler

Hi Jurg, welcome to the PomBAse GitHub tracker. You can reply to the ticket and it will be posted in the tracker. Where is your new ncRNA data?

[bahler]

Danny is working on providing you all the data required for browser (bigwig etc. etc.). But it is not that straightforward and he is very busy.

Cheers, -Jürg

[bahler]

Danny is working on providing you all the data required

[ValWood]

OK we are not in a hurry.... Cheers

Val

On 20/07/2018 17:45, bahler wrote:

Danny is working on providing you all the data required for browser (bigwig etc. etc.). But it is not that straightforward and he is very busy.

Cheers, -Jürg

From: Val Wood [mailto:notifications@github.com] Sent: 20 July 2018 17:41 To: pombase/curation curation@noreply.github.com Cc: Bahler, Jurg j.bahler@ucl.ac.uk; Mention mention@noreply.github.com Subject: Re: [pombase/curation] ncRNAs (#2007)

@bahlerhttps://github.com/bahler

Hi Jurg, welcome to the PomBAse GitHub tracker. You can reply to the ticket and it will be posted in the tracker. Where is your new ncRNA data?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/pombase/curation/issues/2007#issuecomment-406656953, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ANk7VAHlbwHCCcIP7FbJhPS5yidIVhJgks5uIggBgaJpZM4UM-mk.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/pombase/curation/issues/2007#issuecomment-406658266, or mute the thread https://github.com/notifications/unsubscribe-auth/AHBLKDhDDGQ7HsnRNYVjVa8OEANXwUC2ks5uIgkUgaJpZM4UM-mk.

-- University of Cambridge PomBase http://www.pombase.org/ Cambridge Systems Biology Centre http://www.sysbiol.cam.ac.uk/Investigators/val-wood

[Antonialock]

The paper for the ncRNAs with new PomBase systematic IDs is PMID:29914874

[ValWood]

@bahler did you want to move forwards hosting the RNAs?This ticket seems to be stalled waiting for data?

[bahler]

Yes please, will ask Maria to send you gff files. We had decided a while ago to remove all SPNCRNA genes from PomBase, except those which have evidence for function (we are finalizing a paper with phenotypes for many ncRNA mutants). PomBase shows still unbalanced information regarding ncRNAs, in that the old ncRNAS (up to about SPNCRNA15500 are presented, but the more numerous (and often more reliable) new ones (SPNCRNA.2000 to SPNCRNA.7774) are not shown. As discussed, it may be best to only show these in a browser (except for those with functional evidence, we will publish some soon), but this is true also for old ones that are often cryptic and should be removed from PomBase unless there is evidence for function.

[ValWood]

Yes I am a bit confused about what was decided, which ones to remove, whether any are redundant or need merging, what to do with other peoples datasets etc.

I think the best think is first to get all the data hosted as tracks and then evaluate the situation...

I can deal with the UTrs at the same time.

[ValWood]

I will open a new ticket for this issue. I want to keep this thread as an archive but I'll list all of the datasets and questions in a new ticket.

[ValWood]

please refer to the new ticket https://github.com/pombase/curation/issues/2809