T2T chm13 fasta and annotation files

Question

[sarahmanderni]

Hi,

From the link below, I have used GCA_009914755.4.chrNames.fa.gz genome reference (human T2T chm13) for alignment in bowtie2 in an atac-seq experiment.

https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/html/GCA_009914755.4_T2T-CHM13v2.0.description.html

First, is it the correct version of CHM13 to use for this purpose?

If so, can I use the refseq annotation file (GCF_009914755.1_T2T-CHM13v2.0.110.20220412.gtf.gz) available in the same link for annotation of DARs (with homer for instance)?

Apologies for the naive question! Still not sure which source to use after hg38.

Thanks!

Answer 1

[Darked89]

The latest T2T genome version is 2.0, so you should have the correct FASTA version (25 contigs => 1-22, X, Y and MT) plus the bowtie2 etc. indexes.

Depending if you really want to use the latest genome annotation, you may check this CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure.

caveat I have not used as yet the above annotation, so some sanity checking is required.