Hello all,
I have pair-end reads (1.fq and 2.fq ) data and mapped them with 'bwa aln', I don't want to generate alignments in the SAM format in paired-end way with 'bwa sampe', but generate sam format with 'bwa samse' respectively, and then merge the two sam file
bwa aln reference.fa 1.fq > 1.sai
bwa aln reference.fa 2.fq > 2.sai
bwa samse reference.fa 1.sai 1.fq > 1.sam
bwa samse reference.fa 2.sai 2.fq > 2.sam
How to merge 1.sam and 2.sam?
can someone give me suggestions? thanks!
I have pair-end reads (1.fq and 2.fq ) data and mapped them with 'bwa aln', I don't want to generate alignments in the SAM format in paired-end way with 'bwa sampe', but generate sam format with 'bwa samse' respectively, and then merge the two sam file
bwa aln reference.fa 1.fq > 1.sai
bwa aln reference.fa 2.fq > 2.sai
bwa samse reference.fa 1.sai 1.fq > 1.sam
bwa samse reference.fa 2.sai 2.fq > 2.sam
How to merge 1.sam and 2.sam?
can someone give me suggestions? thanks!
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