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Old 06-11-2010, 02:12 AM   #1
AvinashP
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Location: India

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Default Input to BWA from multiple Lanes

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.
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Old 06-11-2010, 07:31 AM   #2
drio
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I assume the data from different lines belongs to the same sample. If so, yes, you can merge the BAM files per each line (picard tools) and align with BWA.
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Old 06-11-2010, 09:24 AM   #3
swbarnes2
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You can use Unix cat to combine files. At the command line, enter "cat file 1.fq file2.fq > combined_file.fq
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