Admin: Jennifer Hillman Jackson

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Email:
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Jennifer Hillman-Jackson

Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org

Posts by Jennifer Hillman Jackson

<prev • 4,495 results • page 1 of 450 • next >
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Answer: A: DESeq in Galaxy
... Answered at https://www.biostars.org/p/236997/ ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: Where to get SNPs and Indels?
... Hello, Assign the database "hg19" to the BAM datasets. This is how certain tools interpret the reference genome. I am assuming that you have installed this reference genome on your server already or it exists on the server you are working on. Click on the pencil icon for the dataset to make the ch ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: FastQC Fatal Error: Exit code 1 ()
... Hello, In a default [Galaxy release 17.01 local][1], this tool installs and executes correctly. My guess is that the tool installation failed to complete correctly. Try uninstalling and reinstalling. If that does not work, please share more details. What version of Galaxy are you running? Are you ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: How to generate consensus sequence from a sorted and aligned to ref BAM file?
... Hello, Coverage data can be calculated for BAM datasets using several tools. At http://usegalaxy.org, search in the tool panel with the keywords "bam coverage" or simply "coverage" (no quotes) to find these. Assembly is different and doesn't always mean the same thing. Some tools generate an actua ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: Bowtie mapping has a unmapped gap on chromosome 6
... Hello, I suggest double checking that the tool version, all inputs (include reference data), and settings were exactly the same between the original run and the rerun. If the above checks out, my next troubleshooting guess is that the genome index the tool is accessing has a problem. Where are yo ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: MAF to VCF showing Indels and snps
... Hello, There are several line command tools to convert MAF to VCF format, but none are wrapped for Galaxy yet (or at least not publically shared in the [Main Tool Shed][1]). If curious about using the line-command choices, please review Q&A at https://www.biostars.org or just google with "maf t ...
written 3 days ago by Jennifer Hillman Jackson21k
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Comment: C: Compute and correct GC bias
... Hello souradeep.mis! Questions similar to yours can already be found at: about compute and correct GC bias We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply below. We'll be happy to talk ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: I used tophat and give mistake Error: segment-based junction search failed with
... Hello, As far as I can tell, the error is with this specific version of Tophat when run on MAC OSX when the junction search option is used. A google for the error shows that many have run into this even when running the tool line command (outside of Galaxy). This indicates that this is not a Galax ...
written 4 days ago by Jennifer Hillman Jackson21k
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Answer: A: Installation of new tools in Galaxy
... Hello, Please see this prior Q&A for help troubleshooting: https://biostar.usegalaxy.org/p/11449/ Specifically, [**Planemo**][1] is a highly recommended resource for tool development. Thanks! Jen, Galaxy team [1]: https://planemo.readthedocs.io/en/latest/ ...
written 4 days ago by Jennifer Hillman Jackson21k
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Answer: C: How to export a list of 8 dataset pairs in galaxy
... For those interested in dataset collections, this is the most current tutorial: https://new.galaxyproject.org/tutorials/collections/ ...
written 4 days ago by Jennifer Hillman Jackson21k

Latest awards to Jennifer Hillman Jackson

Scholar 11 days ago, created an answer that has been accepted. For A: Upload to the Galaxy ftp server
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 13 days ago, created an answer that has been accepted. For A: Help with intersect -BedTools, WindowBed
Scholar 21 days ago, created an answer that has been accepted. For A: Extract Genomic DNA error with custom genome
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 5 weeks ago, created an answer that has been accepted. For A: HTseq runs fail
Scholar 8 weeks ago, created an answer that has been accepted. For A: DEPRECATED tools in Galaxy
Scholar 9 weeks ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Scholar 11 weeks ago, created an answer that has been accepted. For A: fastq-dump on Galaxy?
Scholar 3 months ago, created an answer that has been accepted. For A: Reads on Y chromosome while doing sequecing with a female donor
Scholar 4 months ago, created an answer that has been accepted. For A: Too few reads after VarScan on RNA-Seq data?
Scholar 4 months ago, created an answer that has been accepted. For A: extrect sequences according to a tabular
Scholar 5 months ago, created an answer that has been accepted. For A: Can't see histories shared with me
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 6 months ago, created an answer that has been accepted. For A: Help with intersect -BedTools, WindowBed
Popular Question 6 months ago, created a question with more than 1,000 views. For Welcome to Galaxy Biostar
Scholar 7 months ago, created an answer that has been accepted. For A: Why are the SOLiD mapping functions gone?
Scholar 7 months ago, created an answer that has been accepted. For A: Upload to the Galaxy ftp server
Scholar 7 months ago, created an answer that has been accepted. For A: alignseq.loc and the use of 2bit files
Scholar 8 months ago, created an answer that has been accepted. For A: How to delete workflow from list of published workflows
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 8 months ago, created an answer that has been accepted. For A: Extract gene sequence from BAM.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available

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