Post date: May 09, 2014 5:6:14 PM
# First, I needed to make my fasta file (from the de novo assembly) look like a fasta file, not a fastq file. See script fastq2fasta.pl in /labs/evolution/projects/sosorum at USU.
# Then I indexed my reference sequence on the cluster here. See jobsubIndex.sh. To run it:
qsub jobsubIndex.sh
# To check jobs that are running:
qstat
#To run BWA for the alignment, see wrap_qsub_rc_bwa.pl, and type to run:
perl wrap_qsub_rc_bwa.pl E-BS-*fastq