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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madzayasodara •
Hi Madza
Another approach could be
For Compressed output files:
cat *R1*.fastq.gz >> R1.fastq.gz
cat *R2*.fastq.gz >> R2.fastq.gz
For Uncompressed output files:
zcat *R1*.fastq.gz >> R1.fastq
zcat *R2*.fastq.gz >> R2.fastq
Thanks, Persistent LABS
Hi Madza,
Can you give it a try?
For file ending in ...R1_001.fastq.gz
find -name '*R1_001.fastq.gz' | xargs gunzip -c >> all_R1_001.fastq
similarly or file ending in ...R2_001.fastq.gz
find -name '*R2_001.fastq.gz' | xargs gunzip -c >> all_R2_001.fastq
Let me know if it worked for you.
OP asked for uncompressed fastq at the end, so you'll have to add in a gunzip -c ;)
It will be a pain to type (of course with tab completion) all the file names specially when there are say 100 such files and that too for R1 and R2 separately.
Gnu parallel is amazing. I find this more intuitive and easier syntax to remember:
find . -name '*.fastq' | parallel -j 1 'zcat {} > {.}.combined.fastq'
Yes, you are right about that. My code should be altered to capture either R1 or R2 and write output accordingly, and this should then be ran twice slightly modified. Therefore your example is definitely better.
What if we wanted that name of the file is also the name of the output file?
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Hello madzayasodara!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=71842
This is typically not recommended as it runs the risk of annoying people in both communities.
Didn't know this was a prob. Thanks for letting me know. -madza
What if we wanted that name of the file is also the name of the output file?
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