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 • 6,248 results • page 1 of 625 • next >
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Answer: A: Cufflinks C. elegans no gene names?
... Hello, The reference annotation must include the **tss_id, gene_id, and gene_name** attributes to have those values incorporated by this tool. Your annotation file is probably missing: **gene_name**. iGenomes is a common source for annotation data to use with this tool suite. https://support.illum ...
written 51 minutes ago by Jennifer Hillman Jackson24k
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Answer: A: DESeq2 Gene IDs
... Hello, Double check the annotation file that you are using versus the attributes being counted by the upstream tools and by this tool. For gene annotation to be promoted to the DeSeq2 output summaries, the annotation GTF/GFF must contain transcript_id and gene_id within the attributes when HTseq-co ...
written 1 hour ago by Jennifer Hillman Jackson24k
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Answer: A: Job Submission Failed
... Hello, There is likely a problem with the inputs. Please review the troubleshooting and tutorial help below first. Galaxy FAQs: My job ended with an error. What can I do? https://galaxyproject.org/support/tool-error/ Galaxy tutorials: https://galaxyproject.org/learn/ Then if you cannot determin ...
written 1 hour ago by Jennifer Hillman Jackson24k
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Answer: A: Non-coding RNA feature type/attribute
... Hello, The "ID Attribute" is used by the tool to group together annotation lines. My guess is that in your data the common attribute is "MIRNA". Help from the tool form: > GFF attribute to be used as feature ID. Several GFF lines with the > same feature ID will be considered as parts of the ...
written 1 hour ago by Jennifer Hillman Jackson24k
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Answer: A: How to covnvert gene id to gene names
... Hello, Double check your reference annotation file (GTF or GFF3). Make sure it has the attributes **tss_id, p_id, and gene_name**, for full statistics and incorporation of the annotation. Variations of this question have been asked many times before -- so please review the prior Q&A for more d ...
written 1 hour ago by Jennifer Hillman Jackson24k
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Comment: C: problem in directory acquisition
... Hello nishiwaki! Questions similar to yours can already be found at: FTP transfer problems 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 about it. Chee ...
written 2 hours ago by Jennifer Hillman Jackson24k
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Answer: A: Compare 2 BAM files for covarage regions
... Hello, Please see the tools in the group **NGS: DeepTools**. Example usage is covered in these tutorials: http://deeptools.readthedocs.io/en/latest/content/example_step_by_step.html Thanks! Jen, Galaxy team ...
written 2 hours ago by Jennifer Hillman Jackson24k
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Answer: C: Barcode splitter error
... **UPDATE** This is a problem server side at Galaxy Main https://usegalaxy.org. An issue ticket has been created to track the correction, please follow for updates: https://github.com/galaxyproject/usegalaxy-playbook/issues/111 I am not sure yet if the dependency problem is present at the other use ...
written 3 days ago by Jennifer Hillman Jackson24k
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Comment: C: Help with an simple workflow (annotation)?
... Table Blast results are almost in the `interval` format. You will need to subtract 1 base from the start coordinates to make it fully match interval format. Use the tool **Text Manipulation > Compute** to adjust the coordinate and optionally the tool **Cut** to rearrange/pick the final columns to ...
written 3 days ago by Jennifer Hillman Jackson24k
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Answer: A: NG-CHM visulaization tab is not updating
... Hello, For troubleshooting help with the install, try contacting the tool authors. They will know best about how to configure the tool to work in a local Galaxy. Or you could first try following the instructions for the related *heat_map_creation_advanced* tool instead -- it includes more help plus ...
written 3 days ago by Jennifer Hillman Jackson24k

Latest awards to Jennifer Hillman Jackson

Popular Question 3 days ago, created a question with more than 1,000 views. For Re: Mitochondrial Transcripts
Scholar 3 days ago, created an answer that has been accepted. For C: Error using DataManager to fetch a reference genome
Scholar 5 days ago, created an answer that has been accepted. For A: Star-Fusion last-matching gene pairs file
Scholar 11 days ago, created an answer that has been accepted. For A: How to delete workflow from list of published workflows
Popular Question 11 days ago, created a question with more than 1,000 views. For Load Data From Galaxy To Igv
Scholar 11 days ago, created an answer that has been accepted. For A: Error in Galaxy - ''Fatal error: The HTSeq python package is not properly instal
Great Question 13 days ago, created a question with more than 5,000 views. For Get Galaxy! Your own Local Server
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Mapping paired reads to reference genome, variant calling
Scholar 26 days ago, created an answer that has been accepted. For A: Jobs starting to run and then stopping
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to know if mapping to reference genome was succesful?
Scholar 5 weeks ago, created an answer that has been accepted. For A: 'Hidden' Galaxy features which are really useful /
Scholar 5 weeks ago, created an answer that has been accepted. For A: How get Cancer WGS for analysis in Galaxy
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Scholar 6 weeks ago, created an answer that has been accepted. For A: Uploading NCBI Genome
Scholar 7 weeks ago, created an answer that has been accepted. For A: Qiime file not found error
Scholar 7 weeks ago, created an answer that has been accepted. For A: Qiime file not found error
Great Question 7 weeks ago, created a question with more than 5,000 views. For Welcome to Galaxy Biostar
Cylon 7 weeks ago, received 1,000 up votes.
Scholar 7 weeks ago, created an answer that has been accepted. For A: Each sample as a condition? - cuffdiff
Scholar 7 weeks ago, created an answer that has been accepted. For A: Filter SAM or BAM: "unknown reference name" when trying to select multiple chrom
Scholar 8 weeks ago, created an answer that has been accepted. For A: Retrieving nBLAST similarity hits and flanking regions.
Scholar 8 weeks ago, created an answer that has been accepted. For A: Extract Genomic DNA error with custom genome
Scholar 8 weeks ago, created an answer that has been accepted. For A: SAM-to-BAM 'Failed runtime validation of Using reference genome' Error - Local G

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