Post date: Nov 22, 2019 7:55:21 PM
We plan to test of admixture and calculate population recombination rates for the whole genomes (Nature E&E plus 84 more that came with the sperm donor) as part of the revisions for the deletion paper.
Everything needs to be aligned to the melanic genome versions 3. All 384 genomes from the Nature E&E paper are already aligned and in /uufs/chpc.utah.edu/common/home/gompert-group2/data/timema_sp_wgs/files_aln/. These were aligned with bwa mem. IDs for these bugs are in the same directory in WGRS_ids.txt.
I am aligning the 84 genomes sequenced with the sperm donor. The fastq files are in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/SpermDonorPlus
/. There are 3 runs.
Here are examples for all 3 runs (all with bwa version 0.7.17-r1188):
perl ../Scripts/wrap_qsub_slurm_bwa.pl *1.fastq.gz
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/SpermDonorPlus/tcrP150774-run3/
bwa mem -t 8 -k 20 -w 100 -r 1.3 -T 30 -R '@RG\tID:podu_BS_C_458-oaBkIpcE\tPL:ILLUMINA\tLB:podu_BS_C_458\tSM:podu_BS_C_458' /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta WTCHG_256078_303_1.fastq.gz WTCHG_256078_303_2.fastq.gz > /uufs/chpc.utah.edu/common/home/gompert-group2/data/timema_sp_wgs/files_aln/aln_3_podu_BS_C_458-oaBkIpcE.sam 2> /uufs/chpc.utah.edu/common/home/gompert-group2/data/timema_sp_wgs/files_aln/error_3_podu_BS_C_458.log
perl ../Scripts/wrap_qsub_slurm_bwa.pl *1.fastq.gz
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/SpermDonorPlus/tcrP150774-run2/
bwa mem -t 8 -k 20 -w 100 -r 1.3 -T 30 -R '@RG\tID:podu_BS_C_458-ttpYBbRi\tPL:ILLUMINA\tLB:podu_BS_C_458\tSM:podu_BS_C_458' /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta WTCHG_258652_303_1.fastq.gz WTCHG_258652_303_2.fastq.gz > /uufs/chpc.utah.edu/common/home/gompert-group2/data/timema_sp_wgs/files_aln/aln_2_podu_BS_C_458-ttpYBbRi.sam 2> /uufs/chpc.utah.edu/common/home/gompert-group2/data/timema_sp_wgs/files_aln/error_2_podu_BS_C_458.log
perl ../Scripts/wrap_qsub_slurm_bwa.pl *1.fastq.gz
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/SpermDonorPlus/tcrP150774/
bwa mem -t 8 -k 20 -w 100 -r 1.3 -T 30 -R '@RG\tID:podu_BS_C_458-nTaaPXDY\tPL:ILLUMINA\tLB:podu_BS_C_458\tSM:podu_BS_C_458' /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/mod_map_timema_06Jun2016_RvNkF702.fasta WTCHG_251181_303_1.fastq.gz WTCHG_251181_303_2.fastq.gz > /uufs/chpc.utah.edu/common/home/gompert-group2/data/timema_sp_wgs/files_aln/aln_1_podu_BS_C_458-nTaaPXDY.sam 2> /uufs/chpc.utah.edu/common/home/gompert-group2/data/timema_sp_wgs/files_aln/error_1_podu_BS_C_458.log
All of the results will be in files_aln.