Hi all,
I recently have some Gro-seq data. What I want to do is this:
1. Workflow
Counting how many reads per 200bp windows per chromosome. For this, my
work flow is as followed:
fasq - fasq groomer - bowtie - BAM to SAM - interval
BED - 200 bp windows
regional variation - feature
2.
Hello Di Nguyen,
The output of the Feature coverage tool is a tab-delimited file, so it
will work with many of the tools in Statistics, Join, Subtract and
Group, Filter and Sort, and Text Manipulation plus others.
Subtract and Group - Group may be a good place to start. Please see
the
Hello Di,
Yes, the 200 bp windows should be for the reference genome, apologies if
that was not clear.
The idea is to create a simple text file of the chrom-start-stop (one
line per chromosome), upload, convert to BED, then create windows. Or
better and less manually, you can extract the
3 matches
Mail list logo
