Admin: Jennifer Hillman Jackson

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6 years, 9 months ago
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 • 4,615 results • page 1 of 462 • next >
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Answer: A: Switching from fastq to fastqsanger?
... Hello, You are correct - the names/extensions on dataset names do not matter. The metadata assigned to the datasets is the part that needs to be changed. Click on the pencil icon to reassign the datatype for data that is already loaded. If you are not 100% certain the data is already in fastqsan ...
written 15 hours ago by Jennifer Hillman Jackson21k
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Comment: C: MACS2 peak calling error
... Hello Abigail, What is the error message? Jen, Galaxy team ...
written 15 hours ago by Jennifer Hillman Jackson21k
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Comment: C: Error installing Biopython 1.67
... Yes, that is better. Thanks for posting back! ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: Remote job server indicated a problem running or monitoring this job.
... Hello, This can indicate a cluster failure, which means that you should re-run. However, it can also indicate a problem with the inputs. This is fairly common with reported errors. A direct re-run will not solve the problem. Instead, carefully double check the inputs against the instructions on th ...
written 3 days ago by Jennifer Hillman Jackson21k
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Answer: A: CollectInsertSizeMetrics Graph does not open
... Hello, The tool has known issues at http://usegalaxy.org. Follow here for progress on the fix: https://github.com/galaxyproject/galaxy/issues/1692 Thanks, Jen, Galaxy team ...
written 4 days ago by Jennifer Hillman Jackson21k
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Answer: A: Error with storage quota
... Hello, I recalculated quota and usage is now at 0%. Next time, log out then back into Galaxy to do the same. Thanks, Jen, Galaxy team ...
written 4 days ago by Jennifer Hillman Jackson21k
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Answer: A: cufflink trancript analysis
... Hello, If working at http://usegalaxy.org, the job started Friday should have queued and potentially finished by now. The exception would be if you had many large jobs started at the same time, in which case jobs will execute a few at a time. In short, jobs will start up as resource is available an ...
written 4 days ago by Jennifer Hillman Jackson21k
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Answer: A: How to export computation results in Galaxy cloud?
... Hello, Downloading: 1. Individual datasets: Click on the disc icon per-dataset 2. Full individual history: Use the History menu option Export 3. Many more customized options [through the API][1], if you have programming resources. Thanks, Jen, Galaxy team [1]: https://galaxyproject.org/dev ...
written 4 days ago by Jennifer Hillman Jackson21k
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Answer: A: MPileup output errror ALT <X> QUAL 0
... Hello, The input fastq sequence quality is very, very low. It may not be usable. [Run FastQC to review.][1] The quality impacts mapping (very few sequences map at all) plus all downstream steps. GATK tools failing is a known - these are deprecated and not recommended. [Alternative variant detectio ...
written 4 days ago by Jennifer Hillman Jackson21k
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Comment: C: Trinity analysis error before to start ?normalization? fastdump?
... The data are paired end. Consider [obtaining the fastq from SRA ENA][1]. The two links for **Fastq files (galaxy)** will place the forward and reverse reads into your history where they can be input into the Trinity tool form as distinct datasets. [1]: https://www.ebi.ac.uk/ena/data/view/SRR214 ...
written 4 days ago by Jennifer Hillman Jackson21k

Latest awards to Jennifer Hillman Jackson

Scholar 1 day ago, created an answer that has been accepted. For A: Can I get back "Operate on Genomic Interval" on local Galaxy instance?
Scholar 10 days ago, created an answer that has been accepted. For A: DEPRECATED tools in Galaxy
Scholar 21 days ago, created an answer that has been accepted. For C: AddOrReplaceReadGroups Fatal error
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: bowtie2 out of memory
Scholar 6 weeks ago, created an answer that has been accepted. For A: Upload to the Galaxy ftp server
Scholar 6 weeks ago, created an answer that has been accepted. For A: Help with intersect -BedTools, WindowBed
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 7 weeks ago, created an answer that has been accepted. For A: Extract Genomic DNA error with custom genome
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
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: HTseq runs fail
Scholar 3 months ago, created an answer that has been accepted. For A: DEPRECATED tools in Galaxy
Scholar 3 months ago, created an answer that has been accepted. For A: Illumina DNA sequence upload problem
Scholar 3 months ago, created an answer that has been accepted. For A: fastq-dump on Galaxy?
Scholar 4 months ago, created an answer that has been accepted. For A: Reads on Y chromosome while doing sequecing with a female donor
Scholar 5 months ago, created an answer that has been accepted. For A: Too few reads after VarScan on RNA-Seq data?
Scholar 5 months ago, created an answer that has been accepted. For A: extrect sequences according to a tabular
Scholar 6 months ago, created an answer that has been accepted. For A: Can't see histories shared with me
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: HISAT2 - no reference genome available
Scholar 7 months ago, created an answer that has been accepted. For A: Help with intersect -BedTools, WindowBed
Popular Question 7 months ago, created a question with more than 1,000 views. For Welcome to Galaxy Biostar
Scholar 8 months ago, created an answer that has been accepted. For A: Why are the SOLiD mapping functions gone?
Scholar 8 months ago, created an answer that has been accepted. For A: Upload to the Galaxy ftp server
Scholar 8 months ago, created an answer that has been accepted. For A: alignseq.loc and the use of 2bit files
Scholar 9 months ago, created an answer that has been accepted. For A: How to delete workflow from list of published workflows

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