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Old 09-01-2020, 02:27 AM   #1
Kaskere
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Default guzip paired fast.gz files

Hello,
I have a bunch of paired fastq.gz files, and I need to decompress them for further low quality data trimming.
However gunzip command is not working on paired files. Any suggestions?

this is the error output
gzip: file.fastq.gz: unexpected end of file

Thank you!

Last edited by Kaskere; 09-01-2020 at 02:36 AM.
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Old 09-01-2020, 03:51 AM   #2
GenoMax
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Are you sure the files are gzipped (is spite of what the extension says)? What does

Code:
 file one_file.fastq.gz
say?
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Old 09-01-2020, 04:52 AM   #3
Kaskere
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Quote:
Originally Posted by GenoMax View Post
Are you sure the files are gzipped (is spite of what the extension says)? What does

Code:
 file one_file.fastq.gz
say?
myfile.fastq.gz: gzip compressed data, from FAT filesystem (MS-DOS, OS/2, NT)

they are compressed..

These paired end files were obtained after PE Trimmomatics
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Old 09-01-2020, 09:17 AM   #4
Biocomputronics
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Try using "zcat" to see if it can display the file contents like:

zcat file.fastq.gz

If it displays the file contents, then redirect the output to a new file like:

zcat file.fastq.gz > new_file.fastq
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Old 09-01-2020, 10:58 AM   #5
GenoMax
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@kaskere: Were these files compressed using Windows zip program? You may need to use "-S .zip" option for gunzip.
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