Split Fastq into 2 files

landrjos · 08-09-2018, 01:52 PM

Hi All,

I have a fastq file which I would like to split into 2 files with every other read going into the 2 separate files. What would the Split function command line be for this? I am a new to computing, so it you are most explicit that would be helpful.

Best,

anoopkmr · 08-09-2018, 07:57 PM

Found it in a post here:https://stackoverflow.com/questions/...om-a-text-file

"sed
You can accomplish the same thing with sed. devnulls answer shows how to do it with GNU sed. Below are alternatives for versions of sed that do not have the ~ operator:

keep odd lines

sed 'n; d' infile > outfile
keep even lines

sed '1d; n; d' infile > outfile"

landrjos · 08-09-2018, 08:31 PM

Hi anoopkmr,

Thanks for the reply. I made a mistake, I was not clear enough. I would like to partition the odd or even "reads" from a fastq file. The reads are in groups of 4 lines in the fastq file. So I would like read 1 (lines 1-4) to go to file1, and read 2 (lines 5-8) to go to file2, and so on until the whole fastq file is divided into two files, the odd (lines 1-4, 9-12, etc...) output file and the even (lines 5-8, 13-16, etc...) output file.

Not every even line and every odd line going to the output files.

Is there a way to do that?

Best,

anoopkmr · 08-09-2018, 08:55 PM

That makes a lot more sense. Sorry, in my own confusion I thought you were trying something more creative and beyond my understanding.

fastq-dump seems like an option but if you are generating these files from BAMs it might be easier to step back to the previous step and generate them all at once.

Not very useful but I hope it helps. Good luck!

GenoMax · 08-10-2018, 05:00 AM

@landrjos: What you are describing is called an interleaved fastq file where R1 and R2 reads are present in a single file.

You can use reformat.sh from BBMap suite to separate the R1 and R2 reads into their own files.

Code:

reformat.sh in=interleaved.fq.gz out1=R1.fq.gz out2=R2.fq.gz

lethalfang · 09-27-2018, 11:31 PM

Try this:
cat original.fastq | awk 'NR%8==1 || NR%8==2 || NR%8==3 || NR%8==4' > first4s.fastq
cat original.fastq | awk 'NR%8==5 || NR%8==6 || NR%8==7 || NR%8==0' > second4s.fastq

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08-09-2018, 01:52 PM	#1
landrjos Junior Member Location: Virginia Join Date: Aug 2018 Posts: 3	Split Fastq into 2 files Hi All, I have a fastq file which I would like to split into 2 files with every other read going into the 2 separate files. What would the Split function command line be for this? I am a new to computing, so it you are most explicit that would be helpful. Best,

08-09-2018, 08:31 PM	#3
landrjos Junior Member Location: Virginia Join Date: Aug 2018 Posts: 3	Fastq reads are in groups of 4 lines Hi anoopkmr, Thanks for the reply. I made a mistake, I was not clear enough. I would like to partition the odd or even "reads" from a fastq file. The reads are in groups of 4 lines in the fastq file. So I would like read 1 (lines 1-4) to go to file1, and read 2 (lines 5-8) to go to file2, and so on until the whole fastq file is divided into two files, the odd (lines 1-4, 9-12, etc...) output file and the even (lines 5-8, 13-16, etc...) output file. Not every even line and every odd line going to the output files. Is there a way to do that? Best,

08-10-2018, 05:00 AM	#5
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	@landrjos: What you are describing is called an interleaved fastq file where R1 and R2 reads are present in a single file. You can use reformat.sh from BBMap suite to separate the R1 and R2 reads into their own files. Code: reformat.sh in=interleaved.fq.gz out1=R1.fq.gz out2=R2.fq.gz

08-09-2018, 07:57 PM	#2
anoopkmr Junior Member Location: Boston Join Date: Aug 2018 Posts: 4	Found it in a post here:https://stackoverflow.com/questions/...om-a-text-file "sed You can accomplish the same thing with sed. devnulls answer shows how to do it with GNU sed. Below are alternatives for versions of sed that do not have the ~ operator: keep odd lines sed 'n; d' infile > outfile keep even lines sed '1d; n; d' infile > outfile"

08-09-2018, 08:55 PM	#4
anoopkmr Junior Member Location: Boston Join Date: Aug 2018 Posts: 4	That makes a lot more sense. Sorry, in my own confusion I thought you were trying something more creative and beyond my understanding. fastq-dump seems like an option but if you are generating these files from BAMs it might be easier to step back to the previous step and generate them all at once. Not very useful but I hope it helps. Good luck!

09-27-2018, 11:31 PM	#6
lethalfang Member Location: San Francisco, CA Join Date: Aug 2011 Posts: 91	Try this: cat original.fastq \| awk 'NR%8==1 \|\| NR%8==2 \|\| NR%8==3 \|\| NR%8==4' > first4s.fastq cat original.fastq \| awk 'NR%8==5 \|\| NR%8==6 \|\| NR%8==7 \|\| NR%8==0' > second4s.fastq