CHM13
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marbl
The complete sequence of a human genome
Hi Team, I noticed that there is a huge differences between rmsk.bigBed and GCF_009914755.1_T2T-CHM13v2.0_rm.out as shown below: 5,586,304 rmsk.bed (converted from rmsk.bigBed using bigBedTobed) 11,369,721 GCF_009914755.1_T2T-CHM13v2.0_rm.out The difference is more...
guppy v6
Just wanted to ask if there are any plans on releasing a `guppy >= v6` base calling of the reads? Thanks.
I was looking for an ONT raw signal dataset at very high coverage (a few 100X) and the nanopore dataset in this repository seems to be ideal. It is just...
I'm having some issues lifting over using the provided chain files. GATK complains that it can't find the reference sequence, yet I'm not precisely sure why. If you know of...
Dear T2T team, I need help to find the 99 "novel" protein-coding genes as reported in the Science paper (Vol 376, Issue 6588 pp. 44-53), quote: "1956 of the genes...
Thank you for the great effort in genomics! I was wondering if there is already a straight forward way to annotate CADD scores for T2T-CHM13 calls?
Hi, thank you so much for this tremendous contribution to human genome research. We are currently trying to call variants from nanopore reads mapped to T2T as reference which works...
I was looking at the gene annotation files, in particular, http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3 It looks like the file contains multiple problems, mostly touching exons with introns of size 0. I can send...
I'm having trouble using the provided GFF3 annotations from https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v1.1.gene_annotation.v4.gff3.gz Here's what I'm doing: `bcftools csq $VCF -f chm13.draft_v1.1.fasta -g chm13.draft_v1.1.gene_annotation.v4.gff3.gz -O z -o $VCF.csq.vcf.gz` And here's my ouput: ```...
