guzip paired fast.gz files

[Kaskere]

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]

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

 file one_file.fastq.gz

say?

[Kaskere]

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

 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]

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]

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