Need to separate paired-end reads from single fastq file.

Question

[basharatbhat09]

Hi there,

I have paired-end reads (in fastq format) merged in a single fastq file, i need to split them into two files please help,

Data is; @HWI-700463F:192:C9M9YANXX:6:1101:1397:2190 1:N:0:CGATGTAT CGAGGACCATGGACACAGCAGAACAAGATGAAGACACCAGGGCTAGGTAATTCCTTGTGAGGGCAGGACCAGCACTTCTGTGTTGCTGTCCCTATGGGAA + BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

@HWI-700463F:192:C9M9YANXX:6:1101:1397:2190 2:N:0:CGATGTAT GCTTTTTTTGCATAGGCATTACTCAGGATCTGAATGGGTTGGGAGGCCGGTGTGGAAGGTGGTTAGGAGCCCAAAGCTAACTGTTCCCATAGGGACAGCA + BBBBBFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFF<fbffffffffffffffffffffffffffffffffffff&lt;7ffff< p="">

does 1 in "1:N:0:CGATGTAT" means forward read and 2 in "2:N:0:CGATGTAT" mean reverse read..

[iraun]

You have a lot of great friends to ask this question: google, biostars, seqanswers ... This question has been asked several times. I recommend you to try to solve the problems yourself before asking, you'll learn more and you'll feel fully realized. Take a look:

• Biostars
• seqanswers

Answer 1

[bhao.haob]

Hi Basharat, this might be coming too late but I thought this thread Fastq Splitter For Paired End Reads might me useful.