Difference between revisions of "TXGP RNAseq analysis"
From Marcotte Lab
(Created page with " == Scripts == * run-bfast-match.sh <pre>#!/bin/bash FASTA=$1 if -f $FASTA ; then echo "File:",$FASTA for FASTQ in $(ls ../fastq/*.fastq.gz) do BASENAME=$(basenam...") |
(→Scripts) |
||
Line 2: | Line 2: | ||
== Scripts == | == Scripts == | ||
− | * run-bfast-match.sh | + | * run-bfast-match.sh : a script to map csfastq reads to FASTA file. |
<pre>#!/bin/bash | <pre>#!/bin/bash | ||
FASTA=$1 | FASTA=$1 |
Revision as of 14:19, 14 June 2011
Scripts
- run-bfast-match.sh : a script to map csfastq reads to FASTA file.
#!/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