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Old 03-27-2015, 05:54 AM   #1
dena.dinesh
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Default Combinig technical fastq files into a single fastq file

Hi,

I have technical replicate fastq files for some samples. For an example I have technical replicates like control_1a.fastq and control_1b.fastq. I would like to combine these two replicates as a single fastq file and do the same thing for other replicates also. is the following way of doing is right?

cat control_1a.fastq control_1b.fastq > Control_1.fastq

Kindly guide me.
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Old 03-27-2015, 05:59 AM   #2
GenoMax
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If source files are not compressed then that should be fine.

Edit: If files are compressed then see the caveat in post #4.

Last edited by GenoMax; 03-27-2015 at 06:22 AM. Reason: added a caveat
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Old 03-27-2015, 06:03 AM   #3
dena.dinesh
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Quote:
Originally Posted by GenoMax View Post
If source files are not compressed then that should be fine.
Thanks Genomax. What do you mean by source files are not compressed? These were just fastq files and not associated with any zip or tar.
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Old 03-27-2015, 06:15 AM   #4
GenoMax
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Example below is from a recent presentation by Drs. Simon Andrews and Tim Stevens (Babraham Institute, UK).

-----------------------------------
If you have gzipped fastq files then are the following result files equivalent?

Code:
$ cat seq1.fq.gz seq2.fq.gz > all1.fq.gz
$ zcat seq1.fq.gz seq2.fq.gz | gzip -c > all2.fq.gz
Answer is No.

Explanation:

Quote:
Some decompressors (gzip for example) will read all of the data from all1.fq.gz, but others (the java GZipInputStream class for example) will not and will silently finish at the the end of the first concatenated file.
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