TXGP RNAseq analysis
From Marcotte Lab
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