Question: Extraction of compressed dataset?
0
gravatar for dpapaeft
2.9 years ago by
dpapaeft0
dpapaeft0 wrote:

Hi,

I'm trying to analyze the RNAseq dataset I've uploaded on Galaxy but it is not identified as a fastq file. I've uploaded it as a compressed qz file. Do I need to extract it in order to analyze it and if so, how can I do this within Galaxy?

Thank you.

fastq upload compressed gz dataset • 579 views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson23k • written 2.9 years ago by dpapaeft0
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The problem may be the extension of the file. Does it really end with a ".qz"? If so, you probably meant to have this be ".gz". The other extension type is not associated with options for compressing ".fastq" data (to my knowledge).

Best, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson23k
0
gravatar for dpapaeft
2.9 years ago by
dpapaeft0
dpapaeft0 wrote:

Hi, thank you for answering!

Well, it originally had a .gz extension, but Galaxy seems to have extracted it upon uploading and it seems to have identified it as a .fastq file. Meanwhile, I tried to convert and save it as a fastq file with using the edit attributes function just in case, but it still doesn't get recognised as such..

I guess I'll just have to wait till the eurogroup is over.. being greek and all... lol!!!

Anyway, thanks, I'll play around with it till I figure it out. 

ADD COMMENTlink written 2.9 years ago by dpapaeft0

Hi, I am not sure if I understand the problem based on this new reply (that .gz loaded the dataset, uncompressed it, and recognized it as .fastq). This was the goal? Fastq files do need to be uncompressed to use them as datasets (unless modifications were made to a local, etc.). But if you have some other issue to sort out, and plan to work on it, that is good to know. Thanks, Jen

ADD REPLYlink written 2.9 years ago by Jennifer Hillman Jackson23k
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