Split Fastq File In Small Fastq Files - Windows

Question

[deepbiofever]

Hi All,

Is there anyway I can split large FASTQ files into small FASTQ files with defined number of reads under windows environment, I know there are multiple option for unix but did not find anything for windows ?

best Deep

[Peter]

See also duplicate thread on SEQanswers: http://seqanswers.com/forums/showthread.php?t=28989

Answer 1

[Sukhi Singh]

or use some freeware like gsplit. Be remember to give the lines in mutiples of 4 [4 lines per read].

[deepbiofever]

the output comes out in GSD format

Answer 2

[Pierre Lindenbaum]

install http://www.cygwin.org , and use split

Answer 3

[seidel]

If you're familiar with R, you can use the ShortRead library to break the file up into smaller files. It's only a few lines of code. The example below takes a fastq file, breaks it up into sets of 1 million reads, writing the results to incrementally named smaller files:

library(ShortRead)

# set the file (.gz files also work)
yourFile <- "foo.fastq"
fileBaseName <- sub(".fastq$","",yourFile)
# iterate over fastq file
f <- FastqStreamer(yourFile, 1000000)
file_index <- 0
while (length(fq <- yield(f))) {
  newName <- paste(fileBaseName, "_", file_index,".fastq", sep="")
  writeFastq(fq,file=newName)
  file_index <- file_index + 1
}
close(f)

[Sukhi Singh]

This is good if file is to be finally processed in R, but for a series of large fastq files, it won't be efficient like as compare to split.

Answer 4

[Alex Reynolds]

You should be able to do this with Powershell, if you don't want to install Cygwin. Use a read count and a modulus operation on four lines, as Sukhdeep suggests.