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
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
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