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Commit 2e7f9b26 authored by Mike Smith's avatar Mike Smith
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fixed file name errors

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exercises/bwa/bwa_batch.sh
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...@@ -4,16 +4,16 @@ ...@@ -4,16 +4,16 @@
#SBATCH --nodes=1 #SBATCH --nodes=1
## copy data to /scratch and change directory ## copy data to /scratch and change directory
cp reference.fa reads.txt $SCRATCHDIR && cd $SCRATCHDIR cp reference.fa reads.fq $SCRATCHDIR && cd $SCRATCHDIR
## create an index ## create an index
bwa index reference.fa bwa index reference.fa
## perform alignment ## perform alignment
bwa aln -I reference.fa reads.txt > out.sai bwa aln -I reference.fa reads.fq > out.sai
## create SAM file ## create SAM file
bwa samse reference.fa out.sai reads.txt > out.sam bwa samse reference.fa out.sai reads.fq > out.sam
## copy results back ## copy results back
cp out.sam $HOME/embl_hpc/exercises/bwa/ cp out.sam $HOME/embl_hpc/exercises/bwa/
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