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Question: HISAT2 gzip: input_r.fastq.gz: not in gzip format
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gravatar for testtoolshed
17 months ago by
testtoolshed • 30
testtoolshed • 30 wrote:

Hello, I have been trying to use HISAT2 to to align RNA-seq ENCODE data which I download on my device and try upload by filesystem paths as dataset in data library (they are .fastq.gz files) but after loading them I received .fastq files and as a result error in HISAT2 gzip: input_f.fastq.gz: not in gzip format 0 reads 0.00% overall alignment rate. What should I do in that case?

Thanks, Kate
rna-seq gzip hisat2 • 1.3k views
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modified 17 months ago by Jennifer Hillman Jackson ♦ 25k • written 17 months ago by testtoolshed • 30
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gravatar for Jennifer Hillman Jackson
17 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Change the datatype to be fastqsanger instead of fastqsanger.gz.

The actual content and the datatype must be a match or this error comes up. Details: https://galaxyproject.org/support/compressed-fastq/

Double check the data is really in fastqsanger format as well, to avoid other issues. This is how: https://galaxyproject.org/support/fastqsanger/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k
1

I would try importing the data into library again and explicitly setting the type to .fastq.gz (or whatever you have) to prevent Galaxy from decompressing it automatically.

ADD REPLY • link written 17 months ago by Martin Čech ♦♦ 4.9k
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