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.
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!
•
written
by
sarahmanderni
1 answer
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.
Log in to answer this question.
