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?
1 answer
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.
Log in to answer this question.
-
HOMER annotatepeaks.pl
written by jjp55 •
-
dyld : Library not loaded: Reason: image not found
written by jjp55 •
-
Bowtie2 cannot find references
written by jjp55 •
-
What does "-Shu" do in samtools view
written by quiocarbajal •
-
Get Gene symbols
written by Kai_Qi
-
Where can I find the required files to configure the genomic data to run THOR for Arabidopsis?
written by Tatsuya •
-
Illumina EPIC methylation analysis with meffil
written by gunnhelenmoen •
-
Annotation of ChIP-seq peaks after MACS
written by dorota.komar •
-
how the chip-seq is represented?
written by maria •
-
Cufflinks for Arabidopsis.. Ensembl or TAIR 10
written by mfahim •
