When to merge data

[rasmussen]

Dear all,
For a paired end sequencing project sequenced with Illumina highseq2500 I have received 18 files for each direction from our sequencing center (so 2X18 fastq files with 1mio reads in each). My question is should I merge these read files into two big files before aligning them to my reference genome or can I align each pair of sequencing files individually and merge the sam or bam file afterwards, or are both methods ok?

I am planing to map with bwa, but I do not guess that that will make a difference?

Thanks

[bruce01]

See this discussion.

TLDR: if all fastq are from a single library, concatenate and align as single files, otherwise align individually and merge the BAM.

[rasmussen]

Thanks for the link, the data is from the same library I'll concatenate the fastq files and then map them.

Thanks