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Question: problem decompressing gzipped data
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gravatar for jgregguw
11 months ago by
jgregguw • 0
jgregguw • 0 wrote:

After downloading a genome from NCBI as a .gz file, when I go to see the header of the file in Galaxy it shows nothing and gives me the error "Problem decompressing gzipped data". Am I missing a simple unzip step in Galaxy?
compression upload galaxy gz • 433 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by jgregguw • 0
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The methods at NCBI here explain how to extract/download genome fasta and related datasets: https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/

Are you certain that the downloaded datasets were complete and intact before loading to Galaxy? I would suggest uncompressing them locally on your computer to test that out.

Use FTP to upload to Galaxy: https://galaxyproject.org/ftp-upload/. Compressed .gz data should load without problems from this source, however, you could always upload the uncompressed version. But this should not really be necessary if the data is complete/intact.

I also noticed that you had some SRA formatted data loaded. When using the tool Get Data: EBI SRA, choose the link(s) under the table header "FASTQ files (Galaxy)" to import the data instead of the SRA formatted data under the header "NCBI SRA file (Galaxy)": https://galaxyproject.org/support/loading-data/

The FAQs for fastq data preparation/reformatting (as needed) are the first few links here: https://galaxyproject.org/support/#getting-inputs-right

Hope that helps but let us know if you continue to have problems! Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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