I'm interested in generating a fasta file from Ilumina paired reads of my wild
type strain. I have an NCBI reference genome I can assemble against and I have
already uploaded my 2 reads (using the NCBI reference as my genome), used fastq
groomer, aligned them with bowtie and generated my pileup.
Two questions -
1. When I call peaks with MACS on Galaxy I get different results than
if I run MACS on my machine via command line. I'm using default
parameters in both instances.
2. Are there any tools in galaxy for doing de-novo motif analysis of
the peaks that I have called. If not can anyone su
Two questions -
1. When I call peaks with MACS on Galaxy I get different results than
if I run MACS on my machine via command line. I'm using default
parameters in both instances.
2. Are there any tools in galaxy for doing de-novo motif analysis of
the peaks that I have called. If not can anyone su
If it is ChIP-motif you may like to consider
http://motif.bmi.ohio-state.edu/ChIPMotifs/
There are several others but this is my favorite.
Vasu Punj
--- On Fri, 2/25/11, Christopher Futtner wrote:
From: Christopher Futtner
Subject: [galaxy-user] de-novo motif analysis
To: galaxy-u...@bx.psu
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