What is the bin size for Bamcompare?
If I'm working on C elegans chipseq data, for bamcompare is it ok to choose a bin size of 50? Is the choice of bin size determined by size of genome? Particularly smaller genome choose a smaller bin size to get better resolution? Or is it determine by size of peak like if it is broad peak use larger bin size?
1 answer
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this to 1. Bigwigs on the genome browser look ugly with binning, and you could later always bin basepair-resolution bigwigs (binsize of 1) in downstream analysis if necessary. Binning saves space, that's it. I don't like that option.
Log in to answer this question.
More posts like this
-
Adjusting MACS3 --slocal and --llocal parameters for small-genome organisms like S. cerevisiae?
written by kalavattam •
-
CNVkit metrics normal range
written by Mateo •
-
Setting the size for finding motifs using homer
written by gogeni5529 •
-
I do not understand how to get total peaks from MACS2 shown to me. What mistake(s) am I making here?
written by Ronin •
-
Deeptools computematrix of scale region give different result from ref point TSS.
written by Emily •
-
SICER for ChIP-seq broad peaks
written by Marco Pannone •
-
Selection of good quality SRA data for SNP analysis.
written by shreeya.raghunath •
-
Is ChIP-seq control file in peak calling must whole genome size??
written by dhehdqls •
-
MACS2 Nomodel doesnt take the fragment size
written by GK1610
-
question about macs2 --broad-cutoff
written by Yu
