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Question: Output of FLASH can't be read by other tools?
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gravatar for Elizabeth Clare
5 weeks ago by
Elizabeth Clare • 20
Elizabeth Clare • 20 wrote:

Hi,

I have used FLASH to assemble some reads. They are still in FASTq format. However I can't get other tools to recognize that they exist.

So for example, if I try to use the FASTq to FASTa covert they are not in the list of files I can convert. Same with clip or cutadapt if I want to remove adaptors... they are not an option. These tools only recognize the original R1 and R2 files as being available in the history.

Has anyone got a solution or an explanation for this? I am sure I did this a few months ago and it did work.

Thanks Beth
fastq datatype galaxy flash fastqsanger • 54 views
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modified 5 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 5 weeks ago by Elizabeth Clare • 20
1
gravatar for Jennifer Hillman Jackson
5 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Check the datatype assignment. It should be fastqsanger or fastqsanger.gz (not just fastq or fastq.gz). Please be aware that some of the older tools will not work with gz compressed data -- you'll need to uncompress it first if a tool does not recognize it or fails with a format error (pencil icon > Edit Attributes > Convert).

FAQs: https://galaxyproject.org/support/

  • The tool I'm using does not recognize any input datasets. Why?
  • How do I find, adjust, and/or correct metadata?
  • How to format fastq data for tools that require .fastqsanger format?

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 5 weeks ago • written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k
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