Admin: Jennifer Hillman Jackson

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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 • 5,690 results • page 2 of 569 • next >
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Comment: C: "Metadata Is Being Auto-Detected" Stuck In Continuous Loop
... Orphan question from prior galaxy-user mailing list. Recent Q&A in newer post: https://biostar.usegalaxy.org/p/26026/ ...
written 1 day ago by Jennifer Hillman Jackson23k
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Comment: C: Galaxy deleting bcftools_stats pdf output?
... For others that may encounter this problem, the IUC team confirmed that the tool has a known issue, still open, details captured in a PR: Nicola Soranzo @nsoranzo 15:04 @_misshapp_twitter pdf creation in bcftools_stats is broken https://github.com/galaxyproject/tools-iuc/pull/1416 has m ...
written 1 day ago by Jennifer Hillman Jackson23k
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Answer: A: Galaxy Cuffdiff output doesnt correspont the output from manual
... Hello, Yes, the CummeRbund tool wrapped for Galaxy has known issues with the plotting functions. The issue involves the content of the outputs produced by Cuffdiff for CummeRbund, so using the data outside of Galaxy is also going to be problematic right now. The issue is tracked here and a fix is ...
written 2 days ago by Jennifer Hillman Jackson23k
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Answer: A: Error with htseq-count
... Hello, Errors with this tool can come up when the inputs are problematic. - First, use a `GTF` annotation dataset with this tool (`GFF` or `GFF3` are not accepted input formats). - Next, regardless of the source, double check that the format is correct: **[Common datatypes explained][1]** - And ...
written 2 days ago by Jennifer Hillman Jackson23k
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Answer: A: Continuous processing for jobs where metadata is auto-detected
... Hello, Your problem is likely related to these open issues. Please feel free to comment at Github for current status on when the changes will be implemented: - https://github.com/galaxyproject/galaxy/issues/3796 - https://github.com/galaxyproject/galaxy/issues/4319 To workaround the problem: Fi ...
written 2 days ago by Jennifer Hillman Jackson23k
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Answer: A: HTSeq-Count: Unknown error occured
... Hello, On the **htseq_count** tool form set the option "Force sorting of SAM/BAM file by NAME" to "Yes". Sorting can help avoid errors across tools and is good to know about. Not all tool forms include the option to sort, so if you need to sort before using other tools in the future, how-to is ex ...
written 2 days ago by Jennifer Hillman Jackson23k
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Answer: A: Galaxy deleting bcftools_stats pdf output?
... Hi, This might be a tool bug related to dependencies. I checked and it hasn't been reported yet. You can report it to the IUC tool authors two ways: - Ask about the problem at the IUC gitter channel: https://gitter.im/galaxy-iuc/iuc - Report the problem at the tool's development repository under ...
written 2 days ago by Jennifer Hillman Jackson23k
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Answer: A: Matched error with cuffdiff
... Hello, These are the two most common reasons for the error (one or both may be present): 1 - HISAT2 was used for alignment but the option to output data formatted for Cufflinks was not set. https://biostar.usegalaxy.org/p/23367/#23369 2 - There is a genome mismatch problem between some of the inp ...
written 2 days ago by Jennifer Hillman Jackson23k
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Answer: A: Adding a custom genome to a history
... Hello, Please see: https://galaxyproject.org/support/ > [Preparing and using a Custom Reference Genome or Build][1] Thanks! Jen, Galaxy team [1]: https://galaxyproject.org/learn/custom-genomes/ ...
written 2 days ago by Jennifer Hillman Jackson23k
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Answer: A: variable, low alignment rates with HISAT2
... Hello, The very low mapping rates do sound as if they are related to the fastq content. Have you run FastQC? This Galaxy tutorial explains how to run and interpret the results. https://galaxyproject.org/learn/ > [NGS logistics][1]. Any problems could be then be reported back to those doing the ...
written 4 days ago by Jennifer Hillman Jackson23k

Latest awards to Jennifer Hillman Jackson

Scholar 1 day ago, created an answer that has been accepted. For A: Reference genome download - a step-by-step please?
Scholar 14 days ago, created an answer that has been accepted. For A: CummerRbund sqlite input file doesnt correspond to Cuffdiff output
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 15 days ago, created an answer that has been accepted. For A: FASTA QC ON GROOMER DATA :
Scholar 16 days ago, created an answer that has been accepted. For A: Trinity- error setting metadata
Popular Question 21 days ago, created a question with more than 1,000 views. For Getting Started with Galaxy Biostar
Popular Question 23 days ago, created a question with more than 1,000 views. For February 18, 2011 Galaxy Development News Brief
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 27 days ago, created an answer that has been accepted. For A: Trinity- error setting metadata
Scholar 5 weeks ago, created an answer that has been accepted. For A: Retrieve Taxonomic Information
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Fasta Format, Custom Genomes, and GATK Chromosome ordering
Popular Question 6 weeks ago, created a question with more than 1,000 views. For April 8, 2011 Galaxy Development News Brief
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Get Galaxy! Your own Local Server
Scholar 9 weeks ago, created an answer that has been accepted. For A: how to Installing Tools into Galaxy from Tool Shed
Scholar 3 months ago, created an answer that has been accepted. For A: Extract Genomic DNA error with custom genome
Scholar 4 months ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Popular Question 5 months ago, created a question with more than 1,000 views. For Welcome to Galaxy Biostar
Scholar 5 months ago, created an answer that has been accepted. For A: filter by fasta ids
Scholar 5 months ago, created an answer that has been accepted. For A: CuffDiff Replicates - which files do replicates 0, 1, 2 point to?
Scholar 5 months ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Popular Question 5 months ago, created a question with more than 1,000 views. For April 8, 2011 Galaxy Development News Brief
Popular Question 5 months ago, created a question with more than 1,000 views. For Text Editing
Scholar 6 months ago, created an answer that has been accepted. For A: How get Cancer WGS for analysis in Galaxy
Scholar 6 months ago, created an answer that has been accepted. For A: 'Sampling' Bam or BigWig files?
Scholar 6 months ago, created an answer that has been accepted. For A: Aligning more than 2 sequences

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