User: Jennifer Hillman Jackson

Reputation:
310
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Trusted
Location:
Bay Area, CA
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2 hours ago
Joined:
6 years, 10 months ago
Email:
j**@galaxyproject.org

Jennifer Hillman Jackson
Application Support at Galaxy Project
http://galaxyproject.org
http://usegalaxy.org
http://biostar.usegalaxy.org
https://vimeo.com/galaxyproject

Posts by Jennifer Hillman Jackson

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Trinity RnaSeq Protocol Galaxy plateform
... Hello, Please see the reply here: https://biostar.usegalaxy.org/p/25720/ Thanks! Jen, Galaxy team ...
written 14 days ago by Jennifer Hillman Jackson310
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Answer: A: Empty VCF file returned by ANNOVAR on Galaxy
... Reply https://biostar.usegalaxy.org/p/18107/ ...
written 18 months ago by Jennifer Hillman Jackson310
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Comment: C: How to calculate average coverage for all genes
... Try **NGS: RNA Analysis > htseq-count**. The SAMtools and BEDtool items mentioned in this thread area also wrapped for Galaxy. ...
written 18 months ago by Jennifer Hillman Jackson310
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Answer: A: Galaxy vs Linux Command Line
... Hello, Galaxy will do all of these items as built-in functionality whereas in a custom line-command workflow each would need to be engineered in. Galaxy includes API access for high-through-put analysis (working through the web interface is not the only method). [BioBlend][1] is a popular choice f ...
written 19 months ago by Jennifer Hillman Jackson310
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Answer: A: Screening whole genome sequence data for mutations in regulatory regions of gene
... Hello, I didn't find a post at Galaxy Biostars, but this tutorial should help you to learn about variant calling and downstream annotation in Galaxy. Modify the example tutorial to create a workflow that meets your specific analysis goals. https://github.com/nekrut/galaxy/wiki/Diploid-variant-call ...
written 19 months ago by Jennifer Hillman Jackson310
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Answer: A: problem with using CuffMerge in Galaxy
... Thanks Devon! For any interested, follow the post here: https://biostar.usegalaxy.org/p/17618/ Jen, Galaxy team ...
written 19 months ago by Jennifer Hillman Jackson310
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Answer: A: Galaxy local installation - download reference genomes
... A reply for most of this question is at Galaxy Biostars: https://biostar.usegalaxy.org/p/16334 That reply does not address why the job is running for so long. hg19 as contained at the Galaxy Rsync server is not appropriate for GATK. Use hg_g1k_v37 instead. Where data managers are placing data is c ...
written 21 months ago by Jennifer Hillman Jackson310
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Answer: A: How to get Gene Sequence from BAM file on Galaxy.
... Hello, BEDTools: Intersect BAM alignments with intervals will perform this operation. For the second input use a BED/Interval file that contains the gene location *based on the same reference genome as the first BED input. UCSC could be a source for such a BED file, along with others. See the tools ...
written 23 months ago by Jennifer Hillman Jackson310
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Comment: C: How to use my own genome on UCSC browser?
... Another good choice. Data from Galaxy is also easily visualized within both IGV and IGB. For known genomes, the links are provided in the UI. So if you decide that you want to do some analysis along with the visualization, using both is an option. ...
written 2.7 years ago by Jennifer Hillman Jackson310
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Answer: A: How to use my own genome on UCSC browser?
... Hello, Galaxy (http://usegalaxy.org) has a very robust "Custom Reference Genome" feature that functions with both analysis tools and visualization. This permits nearly any fasta file to be used as a reference genome. Galaxy's visualization browser is called "Trackster".  Start by loading the fasta ...
written 2.7 years ago by Jennifer Hillman Jackson310

Latest awards to Jennifer Hillman Jackson

Supporter 18 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: How to use my own genome on UCSC browser?
Scholar 2.7 years ago, created an answer that has been accepted. For A: How to use my own genome on UCSC browser?
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: How To Know When A Ucsc Annotation Track Has Been Updated
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: How To Know When A Ucsc Annotation Track Has Been Updated
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: How To Know When A Ucsc Annotation Track Has Been Updated
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: How Do I Get The Gene Names From The Chromosome Locations In A Wig File
Autobiographer 4.1 years ago, has more than 80 characters in the information field of the user's profile.

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