Ulmus laevis EAR - #376
Conversation
|
Hi @diegomics, thanks for sending the EAR of Ulmus laevis. |
|
Hi @additive3, do you agree to supervise this assembly? |
|
One student did this curation, let me know if you spot something :) |
|
OK |
|
|
Hi @CaroB-M, do you agree to review this assembly? |
|
@diegomics Generally the assembly is good with no major changes needed, but track information is needed please. |
|
Hi Jo, are you sure about the tracks? Those are showing in my pretext. I will upload the combined map! |
|
@diegomics Haha they are not on shortcuts so I assumed not there..... |
|
I will adhere the shortcut standards for the next one. I'll ping you when the combined is on the folder |
|
I'm just lazy... ;) |
|
TBH.. should be able to open "gap" or "gaps"... |
|
no |
|
@CaroB-M Ok thank you, I will look for the next reviewer on the list :) |
|
|
Hi @CaroB-M, do you agree to review this assembly? |
|
No |
|
@CaroB-M Ok thank you, I will look for the next reviewer on the list :) |
|
|
Hi @additive3, do you agree to review this assembly? |
|
@additive3 Time is out! I will look for the next reviewer on the list :) |
|
|
Hi @JoannaCollins, do you agree to review this assembly? |
|
Ping @additive3, |
|
yes |
|
Thanks for agreeing! |
|
Hi Diego, Thanks for uploading the assembly, its looking good :-). There are a few regions in each hap that require edits: HAP1: SUPER_2: SUPER_2_unloc_1 looks like it might be a hap/false dup based on cov. SUPER_4: 1-532 is a hap dup of the region next to it. Hap dup @ 82.57. SUPER_5: 39.78-40.77 looks like false/hap dup. 40.78-42.64 needs to flip. SUPER_6: looks like 1-18.47 needs to flip. SUPER_7: Unloc_1 looks like false duplication as i can see that this region already exists in hap2. SUPER_8: 0-8.51 needs breaking off and is part of SUPER_13. 0-5.37 of this piece looks like possible hap/false dup of the region on 13 from ~15.17-20.54. 5.48-8.41 of the piece looks to best fit at the beginning of SUPER_13. SUPER_11: unloc_1 looks like hap/false dup. SUPER_12: 8.89-10.43 looks like hap/false dup. HAP2: SUPER_1:9.94-11.06 flips. SUPER_2: 26.61-28.16 is a hap/false dup. SUPER_3: 20.14-21.96 looks like hap/false dup. SUPER_4:9.35-10.52 looks like hap/false dup. SUPER_5: 133.98-end belongs in the repeat on the left end of the scaffold. SUPER_6: 21.21.-22.60 belongs in gap @ 9.03. Then 1-21.16 flips. 22.66-26.08 looks like false dup. 53.44-53.71 ges in the gap @ 54.94. SUPER_7: unloc_1 looks like probable false dup as seems to be 2 copies of region already in hap2 version. 39.06-39.33 goes in the gap @ 39.76. 108.97-110.47 flips and goes in the gap @ 107.15 SUPER_8: unloc_1 looks like hap/false dup. SUPER_9: based on cov unloc_1 is a hap/false dup. 108.38-109.34 needs to flip. SUPER_14: 80.38-83.58 is hap/false dup. It looks like unloc_2 and 3 can be added to the gap @ 85.24. It almost looks like the end from unloc_3 could flip but it is quite difficult to be sure from the data as it is messy around this region. It is difficult to be certain from the individual hap1/hap2 maps what is hap dup and what is false dup which is why i have listed cases where i am not sure as possible hap/false dup. Hopefully it will be much clearer for you to tell in the merged map. It would be great if you could upload this to the EAR so I could take a look :-) If you have any questions please let me know. Best Wishes Jo |
|
Thanks Jo, I'll work on the combined map and share it here asap |
|
Ping @additive3, |
2 similar comments
|
Ping @additive3, |
|
Ping @additive3, |
|
Sorry for the delay guys, I'll try to work on this on the coming days 馃檹 |
|
Ping @additive3, |
|
Any progress with this assembly? |
|
Ping @additive3, |
|
I have a student working on it but it's delayed. I may handle it mayself |
|
Np.. and from my PoV no rush. |
|
Ping @additive3, |
2 similar comments
|
Ping @additive3, |
|
Ping @additive3, |
|
Hi @JoannaCollins @additive3 |
|
Ping @additive3, |
1 similar comment
|
Ping @additive3, |
|
Hi @diegomics and @henryspaul, Apologies for the delay in getting back to you with this. Thanks very much for sending the merged curated map with the corrections. I have had a another look through and made some edits as well. With regard to the regions that we suspected might be hap dups and belonged in the other hap we can see in the merged map that actually these are just duplicated regions from the same hap. Looking at the repeat tracks we can see that these duplications are all in regions of low complexity repeat where we do typically see a drop in coverage compared to the euchromatic sequence. I can also see that over some of these regions coverage is stacked indicating that the region is collapsed. Taking these aspects into account and as there is some ambiguity i think in this case it makes sense to leave in the duplicated regions. I have made a savestate where i have painted up the chrs. One thing to note from looking at the savestate you sent is that if you tag something as haplotig/falseDuplication you do need to move it to the end of the scaffold otherwise you will run into issues when you try to remake the curated.fa. Any questions please don't hesitate to ask Best Wishes Jo |
|
Ping @additive3, |
4 participants
Assembly review request