Hello, I checked the galaxy tutorial for atac-seq and realized that it suggests to use Hg38 canonical genome for human (bowtie2). I wonder which would be its equivalent to NCBI human genome assembly? and is there a specific reason to use the canonical versus GRCh38.p14 for instance?
Hi @Urzula_Franco
Canonical version of the hg38 assembly contains only main chromosomes (autosomes, X, Y) and mitochondrial sequence. The whole assembly also contains unplaced and unlocalised contigs. .p14 refers to a patch. Patches do not disturb chromosome coordinates.
Info for patches (see text below the table) Genome Browser FAQ
Also check
https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19
Hope that helps
Kind regards,
Igor
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