Conversation
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Hi @phuongdoand, thanks for sending the EAR of Schizoporella errata. |
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Hi @diegomics, do you agree to supervise this assembly? |
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ok |
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Hi @gitcruz, do you agree to review this assembly? |
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No |
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@gitcruz Ok thank you, I will look for the next reviewer on the list :) |
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Hi @tommathers, do you agree to review this assembly? |
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@tommathers Time is out! I will look for the next reviewer on the list :) |
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Hi @additive3, do you agree to review this assembly? |
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Thanks for agreeing! |
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Ping @diegomics, |
1 similar comment
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Ping @diegomics, |
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@additive3 @diegomics Please review. I will have a look now |
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There are lots of instances where unloc sequences look an awful lot like haplotigs, but don't show the normal drop in coverage (9_unloc_2, 1_unloc_2, 2_unloc_4). I think these would also explain the high number of 2-copy kmers in the merqury spectra, so they should be removed |
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Thanks for the ping Tom, this one slipped out. I'll take a look today |
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There is a lot of retained haplotypic duplication. Chr1 First 5.4Mb needs removing as haptingand 5.4-6.96Mb needs flipping..some frag reordering required also, 12-20Mb also mixed hap, 40-42.3Mb hap dup, 47Mb-end needs flipping and repeats are hap dup. unloc 1, 2, 4 also hap dup...3 unsure Chr2 6.8-12.7Mb aly hap, 17.14-17.26Mb frag need (re)moving from location, Unloc_1 localises to 27.6Mb it contains unique seq missing, also requires hap dup removing. Unloc_2 haptig indicates possible missing sequence from chrm @21MB, thing the other unloc are also haptigs Chr3 287kb initial frag needs removing, 8.1-16.5Mb mixed hap region, would suggest 19.1-20.2 needs flipping, suggestion of there being hap dup along with unloc_3, suggestion that unloc 1 needs placing but could just be other hap representation. I'd remove all the other unloc. Chr5 2.4-3.26Mb needs some rearragement, possibly haptigs Chr6 20-20.9Mb needs removing as hap dup, haptig issues at 24.2Mb, haplotype assembly issues at 26.6Mb. Chr7 hap issues 3.4Mb, 29.89-29.96Mb haptig needs removing Chr8 8.1-8.26Mb haptig needs removing, 16.94-17Mb haptig needs removing, 22.49-22.55Mb alt hap likely should be removed, 25.33-25.42Mb needs flipping also suggestion of hap errors, would probably remove unloc_1 Chr9 Unloc_1 localises to 15.74Mb and contains unique sequence, also reveals some haptig that needs removing, unloc_2 is haptig and needs removing Chr11 6.73Mb hap dup needs removing, 8.69-11.2Mb retained hap errors also needs some rearragement, 17.72-end needs removing as haptig, unloc_1 is haptig A lot of the tail of small contig look suspisiously like contamination and shows in kmer profile and blob plot |
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Sorry the delay. Thanks for taking a look guys. |
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@tbrown91 I agree that many of the unloc sequences show segments with a haplotype-like signal. However, they don't show a significant coverage drop, which makes it difficult to determine if it's a real haplotype or just a normal duplication. @diegomics No, the sequences were demultiplexed and decontaminated before manual curation, so the plot should be "clean." @additive3 Thank you for the detailed comment, lots of the unloc I placed them as unloc since there is something like a hap-like signal, but the coverage is normal, which I am uncertain about the call to remove them as hap dup.
For the other positions, I will take a closer look to see if there is anything else we could do with them. |
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@phuongdoand please share the savestate |
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Hi @diegomics , here is the current save state. |
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Attention @additive3, the EAR PDF was updated. |
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Attention @additive3, the EAR PDF was updated. |
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Did you produce an updated contact map file? |
Most of these retained hapdup regions show reduced/haploid coverage |
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@additive3 Yes, I made some changes to the contact map and updated it in the EAR report. |
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Ok, I've been through this and removed/marked up haplotypic duplication... it's a bit of a hack job and a compromise because there are clear flips between the two haplotypes and some of the resulting chromosome scaffolds are a mash of both haplotypes in places.. 11 being the worst. The tail of small contigs are also predominantly contamination. I've tagged up some of it but not all contig that need to be removed. Savestate attached: |
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Hi @additive3 , |
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Hi @phuongdoand I have a feeling it is because you (according to the EAR) are using a very old PretextView version and I've added tags that are not found... Ideally I would use the latest version but, let me see if I can redo the save and make it compatible. |
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There might be some mistakes with the EAR report PDF generation, we are actually using PretextView 1.0.3, but yes, I will update it to 1.0.5 and recheck it. |
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@phuongdoand 1.0.3/1.0.5 shouldn't throw errors. |
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Hi @phuongdoand Hopefully this save state works!...once again sorry. just to reiterate, I've not tagged all the contamination, but you can infer with Hi-C contact/coverage what contigs are the contamination. Let me know if access problems still arise :) |
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@additive3 |
Remove 20 haplotigs and 560 scaffolds that are contaminated (mostly Chlorophyta)
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Attention @additive3, the EAR PDF was updated. |
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Hi @additive3 , I have updated the EAR report after removing the haptotigs tagged by you. Also we have run MetaCC v1.2.0 to cluster the scaffold with Hi-C reads and remove 560 scaffolds that are either Chlorophyta (Algae) or Apicomplexa. |
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Hi @phuongdoand |
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Thanks @additive3 for the review. Congrats on the assembly @phuongdoand! After @diegomics confirmation, you can start with the assembly submission to save time. |
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Assembly review request