User: sdbaney

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sdbaney10
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Posts by sdbaney

<prev • 12 results • page 1 of 2 • next >
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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 7 hours ago by sdbaney10 • updated 7 hours 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 3 days 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 3 days 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 3 days 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 3 days ago by sdbaney10
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Fastqsanger to FastQ
... I am trying to run a utility called transrate to assess my trinity assembled files. I am trying to use my trimmed files (trimmomatic files downloaded from galaxy) that are in fastqsanger format but when they are downloaded it seems to be just edited text documents and not any type of sequence file. ...
fastqsanger dataset convert download fastq written 3 days ago by sdbaney10
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Comment: C: Super Transcript Utility in Galaxy
... Hi Jen! I am trying to track this progress and see that it is currently ticketed with an update trinity once in main tool shed to capture the wrapper for this super transcript utility. Is this something I need to do? Or just keep searching for the utility? (thank you for all your help, I really appr ...
written 3 days ago by sdbaney10
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Answer: A: Quality Assessment of RNA de novo assemble (trinity) without reference genome
... I ended up finding a command line program called transrate that runs metrics on the assemblies without a reference genome. It is working very well. Wanted to give an update. ...
written 5 days ago by sdbaney10
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Quality Assessment of RNA de novo assemble (trinity) without reference genome
... Hello, Are there any tools within the galaxy tool shed that would give me a quality assessment of my trinity assembly without using a reference genome (as there is none for my organism)? I ran two assemblies with the same data trimmed with different parameters and I am trying to figure out a way to ...
rna-seq qa illumina trinity written 7 days ago by sdbaney10
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Paired end illumina RNAseq reads - running trinity with paired trimmed files and adding unpaired as single read?
... We have paired end Illumina HiSeq 4000 reads that we are working to remove adaptors and trim bases below our phred cutoff. Trimmomatic has 4 output files from our two input files. Two that are paired and then two that are unpaired. I was originally going to toss the unpaired trimmed files and just r ...
trinity rna-seq written 8 days ago by sdbaney10

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