splitting fastq?

[yaximik]

I wonder if anyone knows about tools that allow splitting large fastq into smaller chunks. I found a couple scripts that split fasta, but not fastq.

[GenoMax]

You can use "split" with the -l option (if your sequences/quality values do not wrap around on multiple lines). Check the manual page for split for more details.

[JackieBadger]

in unix use:

wc -l filename ### gets the number of lines

Then calculate how many lines you want in each smaller chunk to generate clean divisions of the data

Then:

split -l {number of lines to split} filename

[lorendarith]

I also asked the same question before

http://seqanswers.com/forums/showthread.php?t=25568

[mgogol]

Make sure you use numbers that are divisible by 4.

[Jeremy]

If you aren't using Unix, you can get Unix tools by installing Cygwin.
Like people said, fastq is just a text file, anything that can split a text file will split a fastq file.
sed is generally slower than split, but you could try it:

sed -n 'start,endp' infile > outfile

the "p" after "end" means print, the "-n" means only print the selected lines, if you leave it out the original file is copied over and the selected lines appended to it (so don't leave it out).
e.g. you want a file with a million lines starting from the 4 millionth line:

sed -n '4000000,5000000p' infile > outfile