Combinig technical fastq files into a single fastq file

dena.dinesh · 03-27-2015, 06:54 AM

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.

GenoMax · 03-27-2015, 06:59 AM

If source files are not compressed then that should be fine.

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

dena.dinesh · 03-27-2015, 07:03 AM

Quote:

Originally Posted by GenoMax

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.

GenoMax · 03-27-2015, 07:15 AM

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.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
For MAQ: Is there a Tool to convert sanger-format fastq file to illumina-fotmat fastq	byb121	Bioinformatics	6	12-20-2013 02:26 AM
Split Large FASTQ file in small FASTQ files with user defined number of reads Windows	deepbiomed	Bioinformatics	3	04-04-2013 08:14 AM
quality scores in fastq files extracted from sea files	efoss	Bioinformatics	3	02-01-2013 04:09 PM
Concatenate several SRA reads to a single fastq file	krespim	Bioinformatics	5	07-30-2012 09:04 PM
Reduce file size after Illumina FASTQ to Sanger FASTQ conversion?	jjw14	Illumina/Solexa	2	06-01-2010 05:35 PM

03-27-2015, 06:54 AM	#1
dena.dinesh Member Location: Europe Join Date: Feb 2013 Posts: 58	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.

03-27-2015, 06:59 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	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 07:22 AM. Reason: added a caveat