Post date: Sep 26, 2014 8:57:41 PM
I am re-running the genome alignments for the 500 experimental bugs again, but without the indel realignment step (given the problems this caused for Moe's data). The relevant sequence data are in plates 0-4 in /labs/evolution/data/timema/timema_wgrs and the results will be written to assembliesExperiment. Here is the command for one set of paired-end reads.
bwa mem -t 20 -k 20 -w 100 -r 1.3 -T 30 -R '@RG\tID:66562_296\tPL:ILLUMINA\tLB:66562_296\tSM:timemaTC_2C_24787' /home/A01963476/data/timema/draft_genome/draft0.3/mod_lg_timemaGenome.fasta /home/A01963476/data/timema/timema_wgrs/plate4/WTCHG_66562_296_1.fastq.gz /home/A01963476/data/timema/timema_wgrs/plate4/WTCHG_66562_296_2.fastq.gz > /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/aln_4_296_66562.sam 2> /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/error_4_296_66562.log