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Question: Galaxy fastqc contaminant list
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gravatar for galaxyNewbie
9 months ago by
galaxyNewbie • 30
galaxyNewbie • 30 wrote:

Hello...I created a tab separated text file containing a primer name and associated primer sequence, but Galaxy's factqc does not seem to recognize my tab delimited text file format.

  1. Is the format .txt (tab delimited)?
  2. I only have two columns, the primer name and associated sequences.

Thank you!

fastq tabular fastqc contaminant input • 298 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by galaxyNewbie • 30
1
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the format is a two column input, no header, with a tab separating the columns.

Try changing the datatype to tabular.

The tool will then recognize the input. If the jobs fails, then there is a formatting problem with this input (extra spaces, or possibly spaces instead of tabs) or the fastq input (format or the assigned datatype is a mismatch).

FAQs: https://galaxyproject.org/support/#getting-inputs-right

  • How to format fastq data for tools that require .fastqsanger format?
  • Understanding compressed fastq data (fastq.gz)
  • Reformatting fastq data loaded with NCBI SRA
  • Format help for Tabular/BED/Interval Datasets
  • Common datatypes explained
  • The tool I'm using does not recognize any input datasets. Why?
  • How do I find, adjust, and/or correct metadata?

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
1

Thank you Jen. Importing the primer/adapter list as a tabular file was successful.

ADD REPLY • link written 9 months ago by galaxyNewbie • 30
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