I can answer IGV questions, sadly I'm still coming up to speed on
Galaxy.
I've lost track of the original question, but IGV computes a coverage
histogram on the fly, a bit like the Galaxy Track Browser, but you
have to be zoomed in. However, you can also precompute a coverage
histo
Hi Ying,
You're in luck because I've been working with genome browsers lately, so I
think I can help you address your problem. What you're looking for is a
visualization of a coverage histogram for the BAM reads produced by Tophat,
yes?
It turns out that some genome browsers provide this auto
Thank you for the reminder and the encouraging words!
We just released IGB 6.5 (many improvements!) and are planning what to do
next.
Top on the list is to do a better job of supporting Galaxy users by making
it possible to view your "BAM" files in IGB without having to download them
first.
I w
I am not sure about IGB but IGV can take directly Bam files from Tophat
output, so should not be an issue of visualization.
Vasu
--- On Wed, 4/20/11, Ying Zhang wrote:
From: Ying Zhang
Subject: Re: [galaxy-user] get wig file after tophat
To: "Jeremy Goecks"
Cc: "Baxter, Ad
Dear Ann and Jeremy:
We have this discussion long time ago, and I am sorry that I brought it
up here
again. I am just thinking that as Ann said, can we add this tool which convert
bam into wig file into galaxy? Or make a workflow to generate a wig
file from a
bam file generate by tophat? In th
Ying and all;
Nice discussion and lots of great ideas. One other approach is to generate
bigWig files. You can serve these directly from Galaxy and they have
the same advantages as BAM files; they are compressed and individual
regions that be fetched on demand by UCSC.
This tool in the community t
Ying,
You can create a coverage file from a BAM file using this workflow:
http://main.g2.bx.psu.edu/u/jeremy/w/create-coverage-dataset-from-bam-dataset
While this doesn't generate a proper wiggle file, it can be a useful file for
statistical analysis.
I and others have suggested ways to visual
David,
I have been also uisng the IGV like you have suggested.
Vasu
--- On Tue, 2/22/11, David Matthews wrote:
From: David Matthews
Subject: Re: [galaxy-user] get wig file after tophat
To: "Ying Zhang"
Cc: "Baxter, Adam" , galaxy-u...@bx.psu.edu
Date: Tuesday, Februar
HI,
The option you need in IGV tools is "count". You set a window size and this
gives you a tdf file from your sorted bam (or sam) file which is nice and quick
to view on IGV.
Best Wishes,
David.
__
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Dep
I'm a fan of viewing "coverage.wig" files - they give a nice summary of read
distribution over a chromosome.
What I like about the "coverage.wig" file is that it captures the full read
depth at every base. TDF does something different - it summarizes over
(relatively) large regions. (But this can
Hi,
You can get an equivalent visualisation from the IGV viewer by the Broad
Institute - its under IGV tools and generates a tdf file from bam or sam files.
This also gives a quick and easy way of looking at depth at any particular site
and is very accessible.
Cheers
David
On 21 Feb 2011, at
FYI: samtools + bam file + a bit of perl == to wiggle conversion:
https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024318.html
- Original Message -
From: "Ying Zhang"
To: galaxy-u...@bx.psu.edu
Sent: Monday, February 21, 2011 12:39:47 PM
Subject: [galaxy-user] ge
Hi all,
Ann is correct - Tophat does not produce .wig files when run anymore. However,
it's fairly easy to use Galaxy to make a wiggle-like coverage file from a BAM
file:
(a) run the pileup tool on your BAM to create a pileup file;
(b) cut columns 1 and 4 to get your coverage file.
A final not
Hello,
I think I know the answer (sort of) to this question.
This may be because newer versions of tophat stopped running the "wiggles"
program, which is still part of the tophat distribution and is the program
that makes the "coverage.wig" file.
A later version of tophat might bring this back,
Hi:
I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out
that after the tophat analysis, we can not get the wig file from it anymore
which is used to be able to. Do you have any idea of how to still be able to
get the wig file after tophat analysis? Thanks a lot!
Best
Y
15 matches
Mail list logo
