how to combine pair end data into one file

[forget1997]

Hi guys,
I am a new comer for this forum.
I just run pair end sequencing on Illumina hiseq 2000 and got two files. I was wondering how can I combine each read and output into a single file.
Thanks!

[ECO]

Search please!

[lewewoo]

Linux: cat or sth...
Samtools, merge bam...

[Simon Anders]

why would you want to do this?

[cedance]

I guess if you want to use hmmSplicer, then you'll have to merge the paired end reads. The software doesn't support separately yet.

You could just use a basic unix command: cat pe1.fq pe2.fq > pe_merged.fq

[boetsie]

Some assemblers also require paired-end reads in one file, like Velvet and SSAKE. You can check their scripts to combine the paired-end reads into a single file with the scripts shufflesequences.pl and makePairedOutput2UNEQUALfiles.pl.

[Apexy]

Hi forget1997,
In an attempt to answer your question, I would imagine your aim is to generate a file to be used by velveth. Should this be the case, there are two sample perl scripts "shuffleSequences_fasta.pl" (FASTA) & "shuffleSequences_fastq.pl" (FASTQ) that come with the velveth pakage. Provide them with your files and create a third file of shuffled sequences. If this is not what you want, try and explain a little more. Do you want to join Read1 & Read2 into one read? Do you want to combine both files (cedance & lewewoo suggest something to do this). A respond to Simon's question would surely bring you help.