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Question: TopHat input data
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gravatar for mvinas
22 months ago by
mvinas • 20
mvinas • 20 wrote:

Hello, I am trying to analyze ARN-seq, but when I use TopHat my data is not recognized and I can not include them in the analysis. Is it because they do not have "Sanger-scaled quality values with ASCII offset 33"?? or there is another option?.

It says: "no fastqsanger dataset available". But data is already in fastq format...
fastq tools qa input fastqsanger • 599 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by mvinas • 20
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The dataytpe fastqsanger must be assigned to the datasets for the tool form to recognize them as appropriate input.

Double check the data really is in fastqsanger format and assign the datatype or adjust the quality score scaling (the tool that does this will assign fastqsanger in the output). The mapping results will be problematic/incorrect if actual fastqsanger quality scaled input is not used ("Sanger-scaled quality values with ASCII offset 33").

This is how to do all of the above: https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Thanks, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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