ProkRNAseq

Mapping with 'bwa mem'

• Single-end

DB="$WORK/PSEAE.db/bwadb/PSEAE_PA14_genome"
DBNAME=$(basename $DB)
DBNAME=${DBNAME/.fa/}

for FQ in $(ls ../fastq.tx/*PSEABtx_H2O*fastq)
do
  SAM=$(basename $FQ)
  SAM=${SAM/.called.fastq/_called}
  SAM=$SAM"."$DBNAME".bwa_mem.sam"

  $BWA mem $DB $FQ > $SAM
  #$SAM2HIT $SAM
done