Post date: Dec 19, 2013 4:45:59 PM
I am using bwa to align the two new lanes of Timema mapping family sequence data to the draft Timema genome v0.1. Here are the commands for one individual,
bwa aln -n 4 -l 20 -k 2 -t 8 -q 10 -f alnMAP25300.sai timemaGenome MAP25300.fastq
bwa samse -n 1 -r '@RG ID:timema-MAP25300' -f alnMAP25300.sam timemaGenome alnMAP25300.sai MAP25300.fastq
The results will be written to data/timema/timema_mappingfams/NCGR/parsed but I plan to move them to an assembly directory.