Merging illumina paired-end data Lxxx and R1/R2

Question

[euduca]

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

[GenoMax]

Yes you can as long as it is the same sample (which you say it is).

Answer 1

[DG]

Absolutely. Depending on your workflow and exact organism some people chose to align their lanes independently and add read groups to the reads that came from different lanes and then merge the BAM files after having added read groups. This makes sure that you retain some meta-data associated with the sequencing lane. Mostly that is just for some quality control downstream in case you notice anything weird and want to see if there were issues with a particular sequencing lane.