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Old 10-04-2016, 08:50 PM   #1
Madza Farias Virgens
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Default How to decompress several fastq.gz files into one single file?

How to decompress several fastq.gz files and concatenate them into one single .fastq file? There are two kinds of file in the same folder, some ending in ...R2_001.fastq.gz , and others ending in R1_001.fastq.gz. The work is to decompress and concatenate files ending in ...R2_001.fastq.gz into one R2_001.fastq file, and do the same for ...R2_001.fastq.gz files. Really appreciate any help. Thanks -madza
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Old 10-04-2016, 10:03 PM   #2
SNPsaurus
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gunzip decompresses gz files, cat concatenates them, and * is a wildcard. This is all in the Unix command line once you've moved to the directory with the files.
gunzip *R2_001.fastq.gz
cat *R2_001.fastq > combined_R2_001.fastq
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Old 10-04-2016, 11:52 PM   #3
dpryan
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Code:
zcat *R2* > concatenated_R2.fastq.gz
zcat *R1* > concatenated_R1.fastq.gz
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Old 10-05-2016, 03:56 AM   #4
lindenb
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cross posted https://www.biostars.org/p/215053/
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Old 10-05-2016, 04:21 PM   #5
Madza Virgens
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Default Would appreciate if someone with permissions can delete this for me.

Would appreciate if someone with permissions can delete this for me.
Didn't know crossposting was a prob. Thanks. -madza
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