TXGP RNAseq analysis

Scripts

• run-bfast-match.sh

#!/bin/bash
FASTA=$1
if [[ -f $FASTA ]];
then
  echo "File:",$FASTA
  for FASTQ in $(ls ../fastq/*.fastq.gz)
  do
    BASENAME=$(basename $FASTQ)
    BMF=${BASENAME/".fastq.gz"/}".bmf"
    BAF=${BASENAME/".fastq.gz"/}".baf"
    SAM=${BASENAME/".fastq.gz"/}".sam"
    echo "$FASTQ -- $FASTA --> $SAM"
    bfast match -A 1 -n 4 -f $FASTA -r $FASTQ -z > $BMF
    bfast localalign -A 1 -n 4 -f $FASTA -m $BMF > $BAF
    bfast postprocess -A 1 -n 4 -f $FASTA -i $BAF > $SAM
  done
else
  echo "Usage: run-bfast-match.sh <DB fasta file>"
fi