my previous workflow to go from solexa's sequence.txt to maq mapping went like this
maq sol2sanger s_1_sequence.txt w
maq fastq2bfq w reads-1.bfq 2> /dev/null
maq map -u lane1.unmapped reads-1.map maq.bfa reads-1.bfq 2> reads-1.map.log
and i would think that sol2sts2 would run on sequence.txt and the output would directly go to maq map..
maq sol2sanger s_1_sequence.txt w
maq fastq2bfq w reads-1.bfq 2> /dev/null
maq map -u lane1.unmapped reads-1.map maq.bfa reads-1.bfq 2> reads-1.map.log
and i would think that sol2sts2 would run on sequence.txt and the output would directly go to maq map..
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