I have 30 small fastq files from same sample, and I want to merge it into one file. I know the command is
cat file1.fastq file2.fastq > bigfile.fastq
but is there any short cut for doing it? It just looks silly to type 30 file names one by one...
Thank you for any idea!
2 answers
cat file*.fastq > bigfile.fastq
•
written
by
David Langenberger
Be cautious about this approach! Depending on your system, you can enter an endless loop of concatenating the new file to itself. I strictly do:
cat *.fq > merged.fastq** or **cat *.fastq > merged.fq
...or whatever is needed to ensure the pattern does not match the new file being created.
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written
by
Brian Bushnell
Does this happen? My understanding is that shell first parses "*.fq" and at that time "merged.fq" has not been generated yet. I bet a lot of people must have typed "cat *.txt > out.txt". Shell developers should have been aware of such an issue for many years. I could be wrong, though.
Actually, it happened to me once. That's why I put the 'file' as prefix for the input and 'bigfile' for the output. But I didn't know that it is system dependent. Thanks for mentioning it, Brian.
It just looks silly to type 30 file names one by one...
With file globbing
cat file*.fastq > bigfile.fastq
Note: It also works with fastq.gz files. (http://stackoverflow.com/questions/8005114)
cat file*.fastq.gz > bigfile.fastq.gz
Error while using: cat*.R1_unmapped.fq > unmapped_R1.fq
216_7W_Ca1_R1_unmapped.fq
216_9W_Co2_R1_unmapped.fq
218_5W_Pa1_R1_unmapped.fq
218_7W_Pa2_R1_unmapped.fq
[root@psgl unmapped]# cat *.R1_unmapped.fq > unmapped_R1.fq\
cat: *.R1_unmapped.fq: No such file or directory
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