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...") |
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== 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
