Question: HISAT2 gzip: input_r.fastq.gz: not in gzip format
0
gravatar for testtoolshed
11 months ago by
testtoolshed30
testtoolshed30 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 • 619 views
ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson24k • written 11 months ago by testtoolshed30
0
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 11 months ago by Jennifer Hillman Jackson24k
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 REPLYlink written 11 months ago by Martin Čech ♦♦ 4.6k
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