Question

SICER2 (or EPIC) genomes

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3.5 years ago

jjp55 ▴ 20

Hi all,

This is probably a very basic question, but I am trying to use SICER (or EPIC) to analyze my ChIP-seq data. The samples are Arabidopsis, but TAIR10 is not an option for the genome. Does anyone know how I can use a genome not listed?

Genome EPIC ChIP-seq SICER Sequencing • 964 views

ADD COMMENT • link updated 3.5 years ago by ATpoint 85k • written 3.5 years ago by jjp55 ▴ 20

score 0 · Answer 1 · 2021-06-03

See https://github.com/biocore-ntnu/epic2

You either specify a hardcoded genome OR use --chromsizes & --effective-genome-fraction to indicate chromosome length and the effective (=mappable / unqiue) fraction.

https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html says TAIR10 has an effective size of 119481543 so I'd guess that you could use simply --chromsizes 119481543 --effective-genome-fraction 1 as a simple workaround.