User: sdbaney

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sdbaney10
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3 weeks, 2 days ago
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4 months, 1 week ago
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s******@millersville.edu

Posts by sdbaney

<prev • 17 results • page 1 of 2 • next >
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Comment: A: Cuffdiff crashed if I try to use option "Generate SQLite"
... I am also having this problem. ...
written 7 weeks ago by sdbaney10
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Comment: A: cummeRbund SQLite database error from Galaxy main CuffDiff tool
... I am also having this same problem. I've duplicated the run and when I run the data to generate SQLite for cummeRbund it errors but when I disable that function with all else the same, it works perfectly. ...
written 7 weeks ago by sdbaney10
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Comment: C: Problem when running read cufflinks
... Any resolution to this? Getting the same error. ...
written 7 weeks ago by sdbaney10
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HISAT2 Output in Galaxy vs Command Line
... In galaxy, I am given a BAM and BAI file. Does galaxy implement the sorting and index function that I would need to run through SAMtools if ran from the command line? Or does the galaxy HISAT2 output BAM file need to then be sorted and indexed with SAMtools for use in StringTie? ...
hisat2 bam galaxy sort coordinate written 8 weeks ago by sdbaney10 • updated 8 weeks ago by Jennifer Hillman Jackson25k
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Using Galaxy with AWS
... So we have an AWS account in order to compute on some more powerful servers. We are trying to use the Galaxy website interface with this AWS server but every tutorial we follow brings us to a dead end.Eventually we ended up connected to another seemingly public AWS server but not our own. Can someon ...
aws galaxy written 3 months ago by sdbaney10
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Concatenate vs Concatenate (cat) Utility in Galaxy
... I see there are two wrapped tools under the Text Manipulation header for concatenating datasets, which we are trying to do for multiple sample reads to load into trinity. What is the difference between these two tools? ...
text-mani galaxy cat concatenate written 3 months ago by sdbaney10 • updated 3 months ago by Jennifer Hillman Jackson25k
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Answer: A: Paired end illumina RNAseq reads - running trinity with paired trimmed files and
... Thank you!! This gives me a lot of information. Thank you for being so helpful! ...
written 4 months ago by sdbaney10
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Comment: A: Fastqsanger to FastQ
... Here is the log the error is referring to: [2018-06-18 10:49:57.487] [fileLog] [info] quantification processed 0 fragments so far [2018-06-18 10:50:07.385] [fileLog] [info] quantification processed 1000000 fragments so far [2018-06-18 10:50:21.124] [fileLog] [info] quantification processed 20000 ...
written 4 months ago by sdbaney10
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Comment: A: Fastqsanger to FastQ
... (cont. error code) Completed first pass through the alignment file. Total # of mapped reads : 0 # of uniquely mapped reads : 050000000 # ambiguously mapped reads : 0 [2018-06-18 12:23:50.923] [jointLog] [info] Computed 0 rich equivalence classes for further processing [2018-06-18 12:23:50.92 ...
written 4 months ago by sdbaney10
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Comment: C: Fastqsanger to FastQ
... I was able to download it and edit the file to end with .fastq which seemed to recover the data (before, it was a seemingly empty text document). When I use transrate with the raw read sequencing files (illumina RNA seq) mapped against the trinity assembly file, it runs fine (although gives poor st ...
written 4 months ago by sdbaney10

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