cat fastq from different lanes ?!

[fuad193]

Can I cat fastq files from different lanes and then aligned them ?

Example: I have 4 fastq for one sample two forward from lane 1 and two reverese from lane 2.

Can I do the following ?
cat forward_lane_1.fq forward_lane_2.fq >forward.fq
cat reverse_lane_1.fq reverse_lane_2.fq >reverse.fq
bwa sampe ref.fa aln_sa1.sai aln_sa2.sai forward.fq reverse.fq > aln-pe.sam

OR should I align each lane and merge sam like this:

bwa sampe ref.fa aln_sa1.sai aln_sa2.sai forward_lane_1.fq reverse_lane_1.fq > aln-pe_1.sam
bwa sampe ref.fa aln_sa1.sai aln_sa2.sai forward_lane_2.fq reverse_lane_2.fq > aln-pe_2.sam
samtools merge aln-pe_1.bam aln-pe_2.bam >merged.bam

[peromhc]

Yes, cat the together! The 2nd should be fine, too BTW, should yield equivalent results.

[swbarnes2]

Yeah, either way is fine; merging the fastqs or merging the .bams

[fuad193]

Thanks for help

[Heisman]

One caveat is if one of the lanes is of considerably bad quality to the point you may not want to use the data, it would be better to align each separately with different read groups and then merge. But realistically I don't think many people frequently throw away full lanes of data.