User: gozrom

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gozrom0
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Posts by gozrom

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(Closed) Ballgown - is it possible to install it on Galaxy?
... Ballgown - is it possible to install it on Galaxy? I got to the point that all the analysis from HISAT2 to Stringtie merge ran successfully Stringtie was run with output specifically for Ballgown. Is it possible to install ballgown on Galaxy? Thank you ...
rna-seq written 6 months ago by gozrom0
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Comment: C: HISAT2 input to StringTie with UCSC mm10 or ncbi refseq GTF produces error messa
... Although, now I was planning to use ballgown to analyze the results of StringTie merge, and there is no Ballgown on Galaxy, is it possible to install ballgown on Galaxy? Thank you. ...
written 6 months ago by gozrom0
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Comment: C: HISAT2 input to StringTie with UCSC mm10 or ncbi refseq GTF produces error messa
... That's interesting when I change it to run specifically for ballgown it runs fine, but when the output is specific for DESeq2 and EdgeR it gets error messages. ...
written 6 months ago by gozrom0
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HISAT2 input to StringTie with UCSC mm10 or ncbi refseq GTF produces error message
... Hi, there, rerun HISAT2, tried to run Stringtie for TPM, when running only HISAT results as input everything works out, if I use any reference GTF from UCSC it produces error message. Is there a reference GTF that I can download and use with any tool in Galaxy and will work out or it's not an ...
hisat2 stringtie annotation gtf rna-seq written 6 months ago by gozrom0 • updated 6 months ago by Jennifer Hillman Jackson25k
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Comment: C: Cuffdiff error while running RNA seq
... Thank you I'll follow the ticket. Rerun the cuffdiff again after cufflinks on hisat2 specific for cufflinks same error as before - R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free ...
written 7 months ago by gozrom0
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Comment: C: Cuffdiff error while running RNA seq
... I was trying to download mouse transcriptome file in the FASTA format from Ensemble, If you have a different solution that works for that I would use it instead, thanks. ...
written 7 months ago by gozrom0
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Comment: C: Cuffdiff error while running RNA seq
... Trying to use Salmon, there is no tutorial in the link that you have sent, just an explanation of the principle. Any tutorial on salmon? ...
written 7 months ago by gozrom0
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Comment: C: Cuffdiff error while running RNA seq
... Thanks, about the HISAT2 specific for Cufflinks - no, I used default settings, I'll rerun with specific to cufflinks. I'm new to Galaxy, so thank you for the tutorials, so far I used some of it and in some cases just got youtube videos. I used web GUI public server usegalaxy.org Since I never used S ...
written 7 months ago by gozrom0
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Comment: C: Cuffdiff error while running RNA seq
... Side question: If I want to use TPM metrics instead of FPKM what should I use for that in Galaxy. ...
written 7 months ago by gozrom0
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Cuffdiff error while running RNA seq
... Hi, there, I've aligned my reads with HISAT2, then did cufflinks on the aligned read and cuffmerge, the next step of cuffdiff however failed, I tried running it twice and got the same error: R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundation for Statistical Comput ...
cuffdiff rna-seq biomart error written 7 months ago by gozrom0 • updated 7 months ago by Jennifer Hillman Jackson25k

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