Post date: May 07, 2014 3:29:52 PM
The sequence data are now organized by plates with the experimental data in plates 0-4 (plate 0 was the trial run, which I need to look more into). I aligned these data to the draft timema genome V0.3. The alignments are here: /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/. Here is are key commands I used for organizing and aligning the data:
## extracting and moving stuff around, these are examples, all in commandsApril2014.txt
tar -zcvf 130610_SN882_0284_AD26B2ACXX.tar.gz 130610_SN882_0284_AD26B2ACXX/
cp 130624_SN553_0394_BC248HACXX/*fastq.gz plate2/ &
tar -zcvf 130624_SN553_0394_BC248HACXX.tar.gz 130624_SN553_0394_BC248HACXX/ &
cp 130716_SN847_0297_BD28FUACXX/*fastq.gz plate2/ &
##66557,66558 = 130273 = plate2
##66561 = plate3
##66562 = plate4
tar -zcvf 130716_SN847_0297_BD28FUACXX.tar.gz 130716_SN847_0297_BD28FUACXX/ &
cp 130702_SN685_0333_AC24W7ACXX/WTCHG_6454[78]*fastq.gz plate3/ &
cp 130702_SN685_0333_AC24W7ACXX/WTCHG_645[45][90]*fastq.gz plate4/ &
tar -zcvf 130702_SN685_0333_AC24W7ACXX.tar.gz 130702_SN685_0333_AC24W7ACXX/ &
cp 130704_SN228_0394_BC24F7ACXX/WTCHG_65013*fastq.gz plate3/ &
cp 130704_SN228_0394_BC24F7ACXX/WTCHG_65014*fastq.gz plate4/ &
scripts/wrap_qsub_rc_runbwa.pl plate0/*1.fastq.gz
## alignment from /home/A01963476/data/timema/timema_wgrs/scripts/wrap_qsub_rc_runbwa.pl
bwa mem -t 20 -k 20 -w 100 -r 1.3 -T 30 -R \'@RG\\tID:timema1_296\' /home/A01963476/data/timema/draft_genome/draft0.3/mod_lg_timemaGenome.fasta /home/A01963476/data/timema/timema_wgrs/plate1/WTCHG_61246_296_1.fastq.gz /home/A01963476/data/timema/timema_wgrs/plate1/WTCHG_61246_296_2.fastq.gz > /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/aln_1_296_61246.sam 2> /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/error_1_296_61246.log