Arang Rhie
Hello Shane, Thanks for the heads up! Couple years back when I reached out to the 10X team, I have been told to remove 6 Illumina library + 1 padding...
Hello @sstwins21 , I'm afraid I can't access your link :) Would you mind sending that pdf to my email? It's rhiea @ nih.gov with no space. I think it...
Hi @bmansfeld, Fabulous question. :) I am very looking forward to have such a tool become available. Unfortunately, I am not aware of any yet available though. I think it's...
Hi Ben, Very interesting question! It took me some time to think about it - and was drowning with other stuffs ... sorry it took me so long to get...
Hello, The assembly we released [here](https://github.com/marbl/CHM13#v20) has been soft-masked using the repeat models discovered by the T2T team. The associated repeat annotation is available [here](https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.out), as well as in [bed...
This file - https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.t2tRepeatMasker/chm13v2.0_rmsk.bb is the most recent repeat masker track, matching the file I linked in my comment above. Here is the full description: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&g=hub_3267197_t2tRepeatMasker Let us know if...
Thanks Jessica! Ping, FYI, the original T2T RepeatMasker .out file is here: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.out Please use this .out file until we have a better understanding of the .bb file.
Hi Jessen, Thanks for your thoughtful feedbacks. i) Larger genome size than expected Currently, as you might have noticed, the completeness score is computed based on 'distinct' k-mers, with no...
Hi @bredeson, Thanks for sharing your spectra-cn plot! This helped me understand your assembly. Regarding (i) - it seems like your completeness got affected by the little missing k-mer hump...
@faguil you could, depending on which stage you want to re start. There are some files that you may have to manually remove before restarting though in case the restart...