Question: TopHat input data
0
gravatar for mvinas
18 months ago by
mvinas20
mvinas20 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 • 497 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 18 months ago by mvinas20
0
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
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