Details
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Type:
Task
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Status: Open (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
Description
This Galaxy mirror:
http://deeptools.ie-freiburg.mpg.de
implements a number of tools for working with BAM files.
I'd like you to test whether or not their mirror enables IGB visualization of BAM and bigwig files.
To test, use my account:
user name: Aloraine@uncc.edu (note it is case sensitive)
password: (ask me)
I've upload a BAM file for Arabidopsis.
First, make an index for it using samtools index.
Next, run the bamCoverage tool on it, which outputs a bigwig file. To get the genome size, add up the values in genome.txt for Arabidopsis on the IGB Quickload site. You can do it very easily in R - just read in the genome.txt file from the URL and calculate the sum.
Make an issue for this in Jira and link it to the bigwig bug issue I reported.
Thanks and if you have any questions please let me know!!!
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Kyle Suttlemyre [ kyle ] | Ann Loraine [ aloraine ] |
| Description |
This Galaxy mirror: http://deeptools.ie-freiburg.mpg.de implements a number of tools for working with BAM files. I'd like you to test whether or not their mirror enables IGB visualization of BAM and bigwig files. To test, use my account: user name: Aloraine@uncc.edu (note it is case sensitive) password: limo162;tent I've upload a BAM file for Arabidopsis. First, make an index for it using samtools index. Next, run the bamCoverage tool on it, which outputs a bigwig file. To get the genome size, add up the values in genome.txt for Arabidopsis on the IGB Quickload site. You can do it very easily in R - just read in the genome.txt file from the URL and calculate the sum. Make an issue for this in Jira and link it to the bigwig bug issue I reported. Thanks and if you have any questions please let me know!!! |
This Galaxy mirror:
http://deeptools.ie-freiburg.mpg.de implements a number of tools for working with BAM files. I'd like you to test whether or not their mirror enables IGB visualization of BAM and bigwig files. To test, use my account: user name: Aloraine@uncc.edu (note it is case sensitive) password: (ask me) I've upload a BAM file for Arabidopsis. First, make an index for it using samtools index. Next, run the bamCoverage tool on it, which outputs a bigwig file. To get the genome size, add up the values in genome.txt for Arabidopsis on the IGB Quickload site. You can do it very easily in R - just read in the genome.txt file from the URL and calculate the sum. Make an issue for this in Jira and link it to the bigwig bug issue I reported. Thanks and if you have any questions please let me know!!! |
I am unable to view the BAM file since the "View in IGB" link is not available. I attempted to see what version Galaxy they were using by going to
http://deeptools.ie-freiburg.mpg.de/static/welcome.html
and
http://deeptools.ie-freiburg.mpg.de/static/welcome.html.sample
but neither show the version. So I came up with looking at the galaxy.base.js file
deeptools uses
<script src="/static/scripts/galaxy.base.js?v=1399635790" type="text/javascript"></script>
Our internal Galaxy uses
<script src="/static/scripts/galaxy.base.js?v=1397511167" type="text/javascript"></script>
usegalaxy.org uses
<script src="/static/scripts/galaxy.base.js?v=1400077647" type="text/javascript"></script>
So we have an older version running than deeptools. Yet deeptools does not show the view in IGB link.
David says that they may have disabled visualization on their servers.
If they have done this they may also not support http range request which is needed by IGB.