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-   -   guzip paired fast.gz files (http://seqanswers.com/forums/showthread.php?t=95869)

Kaskere 09-01-2020 02:27 AM

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!

GenoMax 09-01-2020 03:51 AM

Are you sure the files are gzipped (is spite of what the extension says)? What does

Code:

file one_file.fastq.gz
say?

Kaskere 09-01-2020 04:52 AM

Quote:

Originally Posted by GenoMax (Post 234679)
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

Biocomputronics 09-01-2020 09:17 AM

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

GenoMax 09-01-2020 10:58 AM

@kaskere: Were these files compressed using Windows zip program? You may need to use "-S .zip" option for gunzip.


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