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Question: Upload fails for larger file, followed by FASTQ to FASTA conversion error
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gravatar for diannemitch
22 months ago by
diannemitch • 0
diannemitch • 0 wrote:

I am trying to generate a FASTA file from a FASTQ file that was generated on an Illumina MiSeq. The data is a 16SRibosomal data, so it does not fall just one genome. When I try to upload these FASTQ sequences to my account so that I can use the FASTA conversion tool, it errors out as "FAILED: Upload content incomplete". Can you please assist? Thank you. -D
get-data software error ftp galaxy upload • 638 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by diannemitch • 0
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try using the FTP method to load fastq data. My guess is that it is over 2 GB in size, which will always fail with a direct browsed-file upload. Once loaded, the datatype cannot simply be "fastq" for the tool to recognize the dataset.

Next, go forward and ensure/test that the data is in fastqsanger format, then assign the type directly or use the Fastq Groomer to set the datatype. Most tools will require fastqsanger as a datatype - if assigned incorrectly, odd tool errors can occur.

How to for both:

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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