hi,
I have paired end data from multiple lanes (illumina pipleine) in qseq format.
i convert all the qseq files to fastq lane wise.
Combine the first sequences in one file and the next sequences in the other file of a particular lane.
Then follow the BWA pipeline i.e.
index the reference, find the suffix array coordinates ('aln') and then use the 'sampe' command to get the sam files.
But since i have data from multiple lanes, so should i just combine the sam files ?
or Follow a different workflow for creation of input files(fastq) for BWA ?
Please provide some suggestions
Thanks.
I have paired end data from multiple lanes (illumina pipleine) in qseq format.
i convert all the qseq files to fastq lane wise.
Combine the first sequences in one file and the next sequences in the other file of a particular lane.
Then follow the BWA pipeline i.e.
index the reference, find the suffix array coordinates ('aln') and then use the 'sampe' command to get the sam files.
But since i have data from multiple lanes, so should i just combine the sam files ?
or Follow a different workflow for creation of input files(fastq) for BWA ?
Please provide some suggestions
Thanks.
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