Moderator: Mo Heydarian

gravatar for Mo Heydarian
Mo Heydarian480
Reputation:
480
Status:
Trusted
Location:
United States
Last seen:
1 week, 4 days ago
Joined:
4 years, 8 months ago
Email:
m*********@gmail.com

Posts by Mo Heydarian

<prev • 68 results • page 1 of 7 • next >
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Comment: C: Problems transferring FASTQ file from EBI to galaxy
... Can you share the issues you are having with switching to NCBI SRA Tools with your analysis? You may have noticed, but if you use NCBI SRA Tools with single entries to retrieve paired end data, both the forward and reverse reads are dumped to the same file. See [here][1] for how to import paired e ...
written 11 weeks ago by Mo Heydarian480
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Answer: A: Workflow cannot run
... I'm also seeing (simple and small) workflows not running on Main. If I choose to run a workflow in a new history, the history is generated, but the jobs don't appear. If I run the workflow within a history the jobs also don't appear. Cheers, Mo Heydarian ...
written 11 weeks ago by Mo Heydarian480
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Answer: A: Problems transferring FASTQ file from EBI to galaxy
... Hello, There are currently issues with data retrieval from EBI SRA, their technical team is working on fixing it. In the meantime, you can use NCBI SRA Tools for SRA data retrieval. See [this][1] post about importing paired end data with NCBI SRA Tools. Hope this helps! Cheers, Mo Heydaria ...
written 11 weeks ago by Mo Heydarian480
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Comment: C: unable to upload data from EBI SRA
... Hello, Please try retrieving data using NCBI SRA Tools. See [this][1] for NCBI SRA Tools usage in importing paired end data. Hope this helps! Cheers, Mo Heydarian [1]: https://biostar.usegalaxy.org/p/21066/#21095 ...
written 11 weeks ago by Mo Heydarian480
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Answer: A: Data import from EBI SRA to Galaxy does not work
... Hello Beata, I am also seeing an extended run time for FASTQ splitter. An alternative to importing data with NCBI SRA Tools -> FASTQ splitter is to run NCBI SRA Tools with a list of SRR IDs, which will import paired end data as separate files corresponding to the forward and reverse reads. Thi ...
written 11 weeks ago by Mo Heydarian480
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Answer: A: Failed Uploads from EBI SRA to import to Galaxy
... Hello, Can you share the first hundred lines of the FastQ files you retrieve from EBA SRA and NCBI SRA? Alternatively, you can check yourself to ensure the reads are formatted the same way. One known issue with the NCBI SRA Tools wrapper is that it imports paired end data as one FastQ file. This co ...
written 11 weeks ago by Mo Heydarian480
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Comment: C: Failed Uploads from EBI SRA to import to Galaxy
... Sorry to hear. You can send the screenshot to mo_at_galaxyproject_dot_org. You can also share a history with examples of failed attempts to import your data with the same email address/username on usegalaxy.org (this will be informative). Cheers, Mo Heydarian ...
written 12 weeks ago by Mo Heydarian480
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Comment: C: Failed Uploads from EBI SRA to import to Galaxy
... Hello, Thanks for the additional information. I just tried importing SRR1027188 with "NCBI SRA Tools -> Extract reads in FASTQ/A format from NCBI SRA" using the default options and was able to successfully import the SRR1027188 fastq file. Can you try again on your end? Cheers, Mo Heydarian ...
written 12 weeks ago by Mo Heydarian480
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Comment: C: Failed Uploads from EBI SRA to import to Galaxy
... Hello, Which Galaxy instance are you using? What error message do you see and do you see it for all datasets you try to import? This information may help reveal the issue and hopefully find a workaround in the meantime. Cheers, Mo Heydarian ...
written 12 weeks ago by Mo Heydarian480
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Comment: C: Failed Uploads from EBI SRA to import to Galaxy
... Hello, I am also seeing failed uploads from EBI SRA. A temporary solution is to use "NCBI SRA Tools -> Extract reads in FASTQ/A format from NCBI SRA". A sidenote: if you're using a custom Galaxy instance, be sure to update SRA tools to version 2.8.0 (earlier versions are not compatible with the ...
written 12 weeks ago by Mo Heydarian480

Latest awards to Mo Heydarian

Scholar 3 months ago, created an answer that has been accepted. For A: cuffdiff conditions related question
Scholar 7 months ago, created an answer that has been accepted. For A: cuffdiff conditions related question
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: cuffdiff conditions related question
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