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Question: Matched error with cuffdiff
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gravatar for annet.kyomuhangi
11 months ago by
annet.kyomuhangi • 10
annet.kyomuhangi • 10 wrote:

Am new to genomic data analysis. Am using galaxy main to analyze RNA-Seq data but Cuffdiff is giving me the following error. Can someone explain what all this means and how to go about it. Thanks

Fatal error: Matched on error
[18:58:46] Loading reference annotation.
[18:58:47] Inspecting maps and determining fragment length distributions.
BAM record error: found spliced alignment without XS attribute
BAM record error: found spliced alignment with
error rna-seq galaxy hisat2 cuffdiff • 331 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by annet.kyomuhangi • 10
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

These are the two most common reasons for the error (one or both may be present):

1 - HISAT2 was used for alignment but the option to output data formatted for Cufflinks was not set. https://biostar.usegalaxy.org/p/23367/#23369

2 - There is a genome mismatch problem between some of the inputs. https://galaxyproject.org/support/chrom-identifiers/

More help for new Galaxy users can be found at:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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