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Question: HISAT2 input to StringTie with UCSC mm10 or ncbi refseq GTF produces error message
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gravatar for gozrom
9 months ago by
gozrom • 0
gozrom • 0 wrote:

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 option?

Thank you.

Roman
rna-seq gtf annotation stringtie hisat2 • 642 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by gozrom • 0

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.

ADD REPLY • link written 9 months ago by gozrom • 0

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.

ADD REPLY • link written 9 months ago by gozrom • 0
0
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

iGenomes is a better, alternate source for reference annotation. Please see this prior post for details: https://biostar.usegalaxy.org/p/26847/#26850

Ballgown is not installed at Galaxy Main https://usegalaxy.org but is available in the ToolShed (here) for use your own Galaxy.

Get Galaxy! options: https://galaxyproject.github.io/

RNA-seq and other Galaxy Tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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