mMarFoi2 EAR

[gitcruz]

Assembly review request

• ToLID: mMarFoi2
• Species: Martes foina
• Project: ERGA-BGE
• Affiliation: CNAG

[erga-ear-bot]

Attention @gitcruz, you have changed more than one file!
Please make sure to update only the EAR PDF file.

[gitcruz]

Hi @diegomics,

I don't understand the automatic bot error. This time I am pretty sure I uploaded just one EAR. Of course, this is inside two folders called Martes_foina/mMarFoi2/

Please let me know if the PR is good and we can assign a reviewer.

Thanks

[diegomics]

Hi @gitcruz
As you can see below, you are trying to merge two files, one for Coenonympha oedippus and the other for Martes foina:

Please remove Coenonympha oedippus from this PR :)

[erga-ear-bot]

Hi @gitcruz, thanks for sending the EAR of Martes foina.
I added the corresponding tag to the PR and will contact a supervisor and a reviewer ASAP.

[erga-ear-bot]

Hi @diegomics, do you agree to supervise this assembly?
Please reply to this message only with OK to give acknowledge.

[diegomics]

Ok

[erga-ear-bot]

*****
EAR Reviewer Selection Process
Date: 2024-10-25 15:00

All Eligible Candidates:

Github ID     | Full Name       | Institution | Total Reviews | Last Review | Active | Busy | Calling Score | Adjusted Score
----------------------------------------------------------------------------------------------------------------------------
bistace       | Benjamin Istace | Genoscope   | 2             | 2024-10-11  | Y      | N    | 1012          | 1062          
auryjm        | Jean-Marc Aury  | Genoscope   | 1             | 2024-10-14  | Y      | N    | 1012          | 1062          
andar27       | Adama Ndar      | Genoscope   | 1             | 2024-10-16  | Y      | N    | 1012          | 1062          
ldemirdj      | Lola Demirdjian | Genoscope   | 1             | 2024-10-23  | Y      | N    | 1012          | 1062          
tommathers    | Tom Mathers     | Sanger      | 3             | 2024-09-30  | Y      | N    | 1005          | 1055          
SarahPelan    | Sarah Pelan     | Sanger      | 3             | 2024-10-04  | Y      | N    | 1005          | 1055          
epaule        | Michael Paulini | Sanger      | 3             | 2024-10-16  | Y      | N    | 1005          | 1055          
joannacollins | Jo Collins      | Sanger      | 3             | 2024-10-23  | Y      | N    | 1005          | 1055          
diegomics     | Diego De Panis  | IZW         | 8             | 2024-10-22  | Y      | N    | 991           | 986           

Selected reviewer: Benjamin Istace (bistace)
The decision was based on:
- different institution ('Genoscope')
- active ('Y')
- not busy ('N')
- oldest review and fewest reviews among the finalists (1062)

[erga-ear-bot]

Hi @bistace, do you agree to review this assembly?
Please reply to this message only with Yes or No by 31-Oct-2024 at 21:00 CET

[bistace]

Yes

[erga-ear-bot]

Thanks for agreeing!
I appointed you as the EAR reviewer.
I will keep your status as Busy until you finish this review.
Please check the Wiki if you need to refresh something. (and remember that you must download the EAR PDF to be able to click on the link to the contact map file!)
Contact the PR assignee for any issues.

[bistace]

Hello @gitcruz,

very nice assembly!

The HiC map is hard to review because there are a lot of intra-chromosomal contacts. However I don't see anything out of place, the telomeres are present at the extremities and coverage also looks normal across the entire chromosomes. To me this looks good to go!

[diegomics]

Thanks @bistace, yes the assembly looks good.
I'm wondering if the small portion near the gap on SUPER_4 @ 46 Kbp should be place in the zone near the gap on SUPER_4 @ 127,3

[gitcruz]

Dear all,

Thanks @bistace for the review!

@diegomics I agree on your comment about SUPER_4 @ 46 Kbp. Despite of being already contigged is likely repetitive sequence (based on ONT coverage) that better fits into the gap at 127,3 Kb.

We will produce a final savestate and place it inside the same folder. Do you think is necessary to produce a new EAR?

Please please accept the PR and merge it when you can. I think we have this genome and its complete mitochondrion ready to submit.

Thanks!
Fernando

[talioto]

It's a tricky region. There are reads spanning from the left side of the gap at 46 to the right side of the gap at 127. I will browse the alignments some more to see where to make the break and join. But after the BG24 sessions today.

[diegomics]

@gitcruz please share the savestate, so we can move forward and approve it to save time ;)

[talioto]

I took care of it. Here is the savestate.

After examining BAM with IGV, I will make precise edit in tpf after pretext-to-tpf, before rapid_join.pl
SUPER_4: 45944201-46296785 => 127401600 in + orientation

[talioto]

Oh and I localized the unloc on SUPER_8 and the unloc on SUPER_Y. No more unlocs or unplaced!

[bistace]

Very nice, seems good to me!

[erga-ear-bot]

Thanks @bistace for the review.
I will add a new reviewed species for you to the table when @diegomics merges the PR ;)

Congrats on the assembly @gitcruz!
Please make sure that the fasta file to upload to ENA is generated based on the final reviewed version of the assembly.

After @diegomics confirmation, you can start with the assembly submission to save time.
The PR will be merged only when the final version of the EAR pdf is available.

[diegomics]

Nice! Thanks @bistace. @gitcruz please go ahead and start uploading the fasta of the last version to ENA. Don't forget to regenerate the PDF in the meantime so we can merge this PR and release the reviewer ;)

[gitcruz]

Dear @diegomics, In this case is it strictly necessary to generate a new EAR recomputing all stats? Thanks. Fernando

…

On Tue, 29 Oct 2024 at 08:41, Diego De Panis ***@***.***> wrote: Nice! Thanks @bistace <https://github.com/bistace>. @gitcruz <https://github.com/gitcruz> please go ahead and start uploading the fasta of the last version to ENA. Don't forget to regenerate the PDF in the meantime so we can merge this PR and release the reviewer ;) — Reply to this email directly, view it on GitHub <#108 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVMJV5TI7HOBNIBM6ZLZ5433DAVCNFSM6AAAAABQTNDLFCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINBTGQ3DSNBYG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[diegomics]

You don't need to regenerate the pretext map and the blobplot, only update gfastats (result should be different) and merqury and busco (not sure it will be different but maybe). And only on the curated assembly!

[gitcruz]

makes sense, Thanks!

…

On Tue, 29 Oct 2024 at 10:02, Diego De Panis ***@***.***> wrote: You don't need to regenerate the pretext map and the blobplot, only update gfastats (result should be different) and merqury and busco (not sure it will be different but maybe). And only on the curated assembly! — Reply to this email directly, view it on GitHub <#108 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVI7VR5L3AHPJ5IROSDZ55FL5AVCNFSM6AAAAABQTNDLFCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINBTGYZDQMZYGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[erga-ear-bot]

The researcher has updated the EAR PDF. Please review the assembly @bistace.

[gitcruz]

Hi @diegomics,

I just uploaded the updated EAR. Could you merge the PR with the main branch?

Thanks,
Fernando