Post date: Aug 30, 2015 1:57:17 AM
Data from 96 sperm from one male are in /labs/evolution/data/timema/sperm/ in the sub-directories 150616_SN882_0488_BC7B14ACXX and 150701_SN882_0494_BC79FAACXX. There are 384 pairs of fastq files total (forward and reverse reads) which correspond to four pairs of files per sperm. I am using bwa mem to align the files to the version 0.3 reference. Here is an example for one individual:
bwa mem -t 20 -k 20 -w 100 -r 1.3 -T 30 -R '@RG\tID:192393_712517\tPL:ILLUMINA\tLB:192393_712517\tSM:timemaSperm712517' /labs/evolution/data/timema/draft_genome/draft0.3/mod_lg_timemaGenome.fasta /labs/evolution/data/timema/sperm/150616_SN882_0488_BC7B14ACXX/WTCHG_192393_712517_1.fastq.gz /labs/evolution/data/timema/sperm/150616_SN882_0488_BC7B14ACXX/WTCHG_192393_712517_2.fastq.gz > /labs/evolution/data/timema/sperm/Alignments/aln_192393_712517.sam 2> /labs/evolution/data/timema/sperm/Alignments/error_712517_192393.log