Admin: Jennifer Hillman Jackson

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21,510
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Last seen:
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Joined:
6 years, 10 months ago
Email:
j**@galaxyproject.org

Jennifer Hillman-Jackson

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

Posts by Jennifer Hillman Jackson

<prev • 4,672 results • page 1 of 468 • next >
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Comment: C: galaxy problm cufflinks
... Hello - Where are you using Galaxy? At Galaxy Main (http://usegalaxy.org) or elsewhere? SAM/BAM data uploaded will have the datatype autodetected and assigned if the settings are left at default. Double checking that this datatype assignment was actually made is the first place to check for a probl ...
written 3 days ago by Jennifer Hillman Jackson22k
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Answer: A: GFF Error: duplicate/invalid 'transcript'
... Hello Raihan, The first duplicate ID reported was "ID=id20522", but the query used with the **Select** tool is bringing up more matches. Maybe your regular expression query with the **Select** tool needs to be more specific? Example: Using the regular expression `^ID=id20522;` with the **Select** ...
written 3 days ago by Jennifer Hillman Jackson22k
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Comment: C: TRINITY taking forever
... A second correction has been made. Please see this post for details: https://biostar.usegalaxy.org/p/22682/#22692 Thanks for testing again and the follow-up. Should you or others have problems again, please let us know. Jen, Galaxy team ...
written 3 days ago by Jennifer Hillman Jackson22k
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Answer: A: How to use cuffmerge and cuffdiff
... Hello, In short, use Cuffmerge to create a "master" GTF dataset, with the input as the result GTF datasets from Cufflinks (all produced in the experiment) plus the reference annotation GTF dataset (if one is to be used). The result from Cuffmerge is the reference annotation GTF input to Cuffdiff. ...
written 4 days ago by Jennifer Hillman Jackson22k
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Answer: A: Problem with Trinity
... Hello, The problem has been corrected. Please see this post for instructions about how to get your Trinity job or jobs started up again. https://biostar.usegalaxy.org/p/22642/#22674 Thanks again for reporting the problem! Jen, Galaxy team ...
written 4 days ago by Jennifer Hillman Jackson22k
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Answer: A: TRINITY taking forever
... Hello, The issue has been corrected with the Trinity connection to Bridges at PSC this morning. Due to the nature of the problem, any current Trinity jobs should be re-run. Use the "rerun" double arrow button within the current gray dataset to start these quickly up as an exact run of the origina ...
written 4 days ago by Jennifer Hillman Jackson22k
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Answer: A: Adding Genome to the list of reference genomes
... Hello, The Custom Genome/Build function will allow any transcriptome/genome to be used in Galaxy with tools. This is how: - Custom genomes explained: https://galaxyproject.org/learn/custom-genomes/ - Video tutorial help: https://galaxyproject.org/tutorials/ngs/#what-if-pre-computed-index-does ...
written 5 days ago by Jennifer Hillman Jackson22k
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Comment: C: Problem in genrating Correlation Plot
... FYI for others: This sub-issue was resolved through email using by explaining the appropriate NCBI SRA retrieval tool (and explaining usage, also available on those tool forms). -Jen ...
written 5 days ago by Jennifer Hillman Jackson22k
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Answer: A: Problems to mapping in Bowtie 2 ??
... Hello, Update: The delays are now resolved. This is the primary post describing the issue and resolution: https://biostar.usegalaxy.org/p/22633/#22654 Thanks! Jen, Galaxy team ...
written 5 days ago by Jennifer Hillman Jackson22k
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Answer: A: Jobs not running
... Hello, Great news! The issues were resolved, this is the primary post describing the issue and resolution: https://biostar.usegalaxy.org/p/22633/#22654 Thanks! Jen, Galaxy team ...
written 5 days ago by Jennifer Hillman Jackson22k

Latest awards to Jennifer Hillman Jackson

Scholar 9 days ago, created an answer that has been accepted. For C: Error using DataManager to fetch a reference genome
Scholar 24 days ago, created an answer that has been accepted. For A: Each sample as a condition? - cuffdiff
Scholar 4 weeks ago, created an answer that has been accepted. For A: Can I get back "Operate on Genomic Interval" on local Galaxy instance?
Scholar 5 weeks ago, created an answer that has been accepted. For A: DEPRECATED tools in Galaxy
Scholar 7 weeks ago, created an answer that has been accepted. For C: AddOrReplaceReadGroups Fatal error
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 10 weeks ago, created an answer that has been accepted. For A: Upload to the Galaxy ftp server
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 10 weeks ago, created an answer that has been accepted. For A: Help with intersect -BedTools, WindowBed
Scholar 11 weeks ago, created an answer that has been accepted. For A: Extract Genomic DNA error with custom genome
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 3 months ago, created an answer that has been accepted. For A: HTseq runs fail
Scholar 4 months ago, created an answer that has been accepted. For A: DEPRECATED tools in Galaxy
Scholar 4 months ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Scholar 4 months ago, created an answer that has been accepted. For A: fastq-dump on Galaxy?
Scholar 5 months ago, created an answer that has been accepted. For A: Reads on Y chromosome while doing sequecing with a female donor
Scholar 6 months ago, created an answer that has been accepted. For A: Too few reads after VarScan on RNA-Seq data?
Scholar 6 months ago, created an answer that has been accepted. For A: extrect sequences according to a tabular
Scholar 7 months ago, created an answer that has been accepted. For A: Can't see histories shared with me
Teacher 7 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: Help with intersect -BedTools, WindowBed
Popular Question 8 months ago, created a question with more than 1,000 views. For Welcome to Galaxy Biostar
Scholar 9 months ago, created an answer that has been accepted. For A: Why are the SOLiD mapping functions gone?
Scholar 9 months ago, created an answer that has been accepted. For A: Upload to the Galaxy ftp server

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