Hi.

I received paired-end illumina data for some DNA sequencing (Hiseq). There are four fastq files and are named like this:

Fungal_L001_R1_001.fastq and Fungal_L001_R2_001.fastq
Fungal_L002_R1_001.fastq and Fungal_L002_R2_001.fastq

They are from the same library (TruSeq LT DNA kit, insert size of 800-900bp).

Can I merge the R1 and R2 files from different lanes? And so, work normally with the post processing (trimming, assembly, etc.)

Like this:

$ cat Fungal_L001_R1_001.fastq Fungal_L002_R1_001.fastq > Fungal_R1.fastq
$ cat Fungal_L001_R2_001.fastq Fungal_L002_R2_001.fastq > Fungal_R2.fastq

Thanks =)

Duca