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Question: Problem in using uploaded files
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gravatar for sichaves
23 months ago by
sichaves • 0
sichaves • 0 wrote:

I have uploaded a FastaQ (about 300 Mb) but it is not available for choosing in any analysis toll. The upload seems ok, as I did not get error messages and the file name appears in a green box in the history.

Am I missing something in the workflow to make the file available?

Thanks Sandra
galaxy • 751 views
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modified 23 months ago by chen.randy • 110 • written 23 months ago by sichaves • 0
1
gravatar for Jennifer Hillman Jackson
23 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The datatype needs to be assigned to .fastqsanger for most tools to recognize the fastq dataset. This is how to check, adjust quality scores (if needed), and assign: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Hope this helps! Jen, Galaxy team
ADD COMMENT • link modified 23 months ago • written 23 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jenny,

You mean, manually change the datatype of FastQC output file (one of the two file - Rawdata), if it passed the score when using FastQC?

ADD REPLY • link written 23 months ago by bon1068 • 30

This is about changing the input fastq dataset's datatype.

Both of the other answers are correct, but are dependent on the starting input fastq dataset(s) quality score scaling. Sometimes directly assigning type is OK - sometimes the data should be Groomed.

The wiki section immediately below the one linked about explains how to do the checks, and those checks involve the use of the tool FastQC. https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

ADD REPLY • link modified 23 months ago • written 23 months ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for bon1068
23 months ago by
bon1068 • 30
bon1068 • 30 wrote:

It works by just changing manually the datatype of the uploaded FASTQ file from "fastq" to "fastqsanger".
ADD COMMENT • link written 23 months ago by bon1068 • 30
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gravatar for chen.randy
23 months ago by
chen.randy • 110
chen.randy • 110 wrote:

If you know the quality score is good for those FASTAQ, you could upload it by using the format "fastqsanger" initially, with the selected genome database (e.g. hg19).
ADD COMMENT • link written 23 months ago by chen.randy • 110
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