Question: Upload fails for larger file, followed by FASTQ to FASTA conversion error
0
gravatar for diannemitch
22 months ago by
diannemitch0 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

ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 22 months ago by diannemitch0
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 93 users visited in the last hour