Splitting Odd and Even Reads from FastQ to Seperate Output Files

Question

[landrjos]

Hi All,

I have a bioinformatics question. I would like to partition a fastq file into 2 separate output files with odd reads (lines 1-4, 9-12, etc....) into a odd output file (file1) and even reads (lines 5-8, 13-16) into a even output file (file2). Does anyone know a Split command which would do this? I am a newbie to terminal commands this complex.

Best,

Jos

Answer 1

[5heikki]

awk '{if(NR<5){print $0 > "file1.fq"}else{print $0 > "file2.fq";if(NR>7){NR=0}}}' input.fq