MACS2 for Nicotiana tabacum

Question

[970558734]

hello ,

I want to analysis my Nicotiana tabacum chip-seq data with MACS2.My sequence type is single-ended 50. The 'genome' I used is composed of scaffolds,"ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/assembly/Ntab-K326_AWOJ-SS.fa.gz". Can I properly analyzed it in this situation ? How long the 'GSIZE' I should set ?

Thanks!

Answer 1

[dariober]

Unless your genome is in very very short scaffolds, say the size comparable to a peak (100s of bases), I don't see a problem with that.

About effective genome size, have a look at epic-effective. In practice the effective genome size you set shouldn't matter that much. Depending on how complete and repetitive it is, something like "genome size * 0.7" should do in most cases.

EDIT: Just looked at the contig size for the genome in question and it does appear to be highly fragmented