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Question: Fwd: Visualisation Of A Bam File
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gravatar for DeQuincy Prescott (UCL)
6.7 years ago by
DeQuincy Prescott (UCL) • 10
DeQuincy Prescott (UCL) • 10 wrote:
Test of forward email. DeQuincy Prescott Sen Res Tech to Professor Bhattacharya about our group http://tinyurl.com/3264vn Mobile: +44 (0) 7590 695 435 Office: +44 (0) 207 608 6951 Begin forwarded message:
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modified 6.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.7 years ago by DeQuincy Prescott (UCL) • 10
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gravatar for Jennifer Hillman Jackson
6.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, I was able to create a visualization using hg19 as the reference and load this dataset and visualize it. It is important to allow the BAM file to index fully, do not navigate away from the page while this is going on. As a test, I also used SAMTools BAM-to-SAM, then SAM-to-BAM (with hg19), to see if there would be any errors (indicating that an incorrect genome was used), but there were none. This sorted BAM file also visualized fine. Once you had the hg19 visualization created, and the BAM file added as a dataset, there are two key items to change. The first is to set the chromosome to chr22. The second is to set the display. Hover over the buttons next to the track name, click on the display options button, and uncheck the button where only differences are displayed. For analysis, please see the tools in the groups NGS: Indel Analysis and SAMTools Mpileup. On the test server (http://test.g2.bx.psu.edu/) under NGS: Variant Detection, an unsupported version of FreeBayes is available (with VCF output). More about SNP analysis is linked from this page (first set of links under "Other exercises"): http://main.g2.bx.psu.edu/u/james/p/exercises. Using the tool search and entering "SNP" as a keyword will locate more tools. All tool on the main server have help on the tool form and links to documentation. Best wishes for your project, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k
Visualization dataset index correction, please see below: I stated this incorrectly. Once a dataset starts indexing, it will complete successfully even if the visualization is saved and/or closed. -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD REPLY • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k
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