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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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Effective genome size T2T-CHM13 reference genome #1284

Closed smsamin closed 10 months ago

smsamin commented 10 months ago

Hi,

I was wondering to ask if its possible to update the effective genome size table (https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html) for the new human reference genome T2T-CHM13 based on the read length for processed bam files. Thanks so much in advance!

ecroot commented 10 months ago

I would also find this useful please - I have tried running faSize and faCount on a copy of the hs1 genome fasta file, but either due to the "complete" nature of t2t or something I'm doing wrong, I'm getting an effective genome size exactly the same as the genome size

WardDeb commented 10 months ago

Hi both,

The latest develop version has these tables updated (both for the non-N count as the khmer approximation), main branch will be updated when the other features are ready to implement. Note that T2T indeed has no N's so for the first method the ESS coincides with the actual genome size.

Feel free to reopen if something is still unclear !

WardDeb