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How to use GWIPS for viewing personal bam file
23-Jan-2015, 09:25 AM
Post: #1
How to use GWIPS for viewing personal bam file
Thanks for GWIPS-viz, it is a good tool to view ribosome RNA and mRNA for the different tracks. I just a little question: can I use the GWIPS-viz to compare my personal ribosome profiling data? Now I had two bam file (mRNA and Ribosome profiling RNA respectively) that after tophat alignment. I have no idea how to upload my data and compare them by GWIPS-viz. All kinds suggestion are appreciated.
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23-Jan-2015, 09:34 AM
Post: #2
RE: How to use GWIPS for viewing personal bam file
Hi,

Thanks for your feedback on GWIPS-viz.

While you cannot directly upload your personal bam files as custom tracks in GWIPS-viz yet, we propose the following work-around:

1. Click on the "RiboGalaxy" link on the LHS of the GWIPS-viz home page or go directly to http://ribogalaxy.ucc.ie .
2 .Upload your bam files under the "Get Data" section.
3. Then use convert "BAM to BigWig" under the "Convert Formats" section.

The BigWig output should provide a link directly to GWIPS-viz to view your data as a custom track.

If you have any problems, let us know through this forum and we would be happy to try to help.

Thanks for your interest in GWIPS-viz,
Audrey
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24-Jan-2015, 02:22 AM
Post: #3
RE: How to use GWIPS for viewing personal bam file
(23-Jan-2015 09:34 AM)audrey Wrote:  Hi,

Thanks for your feedback on GWIPS-viz.

While you cannot directly upload your personal bam files as custom tracks in GWIPS-viz yet, we propose the following work-around:

1. Click on the "RiboGalaxy" link on the LHS of the GWIPS-viz home page or go directly to http://ribogalaxy.ucc.ie .
2 .Upload your bam files under the "Get Data" section.
3. Then use convert "BAM to BigWig" under the "Convert Formats" section.

The BigWig output should provide a link directly to GWIPS-viz to view your data as a custom track.

If you have any problems, let us know through this forum and we would be happy to try to help.

Thanks for your interest in GWIPS-viz,
Audrey

Hi Audrey,

Thanks very much for your detail reply. The propose work-around is very helpful for me. Thanks again.

Best,
Shang-Qian
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04-Jan-2016, 10:33 AM
Post: #4
RE: How to use GWIPS for viewing personal bam file
An update to this question, BAM files can now be directly uploaded as custom tracks in GWIPS-viz.

Use the format
track type=bam name="bam Example One" description="A bam file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam

See link below for more details:

https://genome.ucsc.edu/goldenpath/help/...Track.html
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