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Question: Uploading Gz Files
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gravatar for Keith Giles
8.7 years ago by
Keith Giles • 50
Keith Giles • 50 wrote:
I am unable to load the raw alignment data from the broad institute datasets available from the ucsc downloads section. the data is in the gz format. any suggestions on how to get it uploaded?
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modified 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k • written 8.7 years ago by Keith Giles • 50
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gravatar for Daniel Blankenberg
8.7 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:
Hi Wei, 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. Thanks, Dan
ADD COMMENT • link written 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k
Hi Dan, Many thanks for your reply. I just upload the file from my computer and browse the location. If I upload the zip compressed file, should I choose txtseq.zip format? My data is fastq file in txt file. And how could I put the file in a web-accessible location? You mean the FTP server? Thanks for your help! Wei
ADD REPLY • link written 8.6 years ago by Yanwei Tan • 40
Hi Wei, To upload a gzipped file (e.g. somefile.fastq.gz), just upload as you normally would (don't set to txtseq.zip - this is a special format), the file will be ungzipped automatically; zip files are not yet supported. As far as a web-accessible location, you can specify http(s) and ftp locations by entering e.g. http://someserver.org/somefile.fastq or ftp://someserver.org/somefile.fastq into the 'paste' box in the upload tool, if you have access this type of resource. Thanks, Dan
ADD REPLY • link written 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k
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