Commit 658c7415 authored by peguerin's avatar peguerin
Browse files

alignments.fof

parent fe845d7d
......@@ -14,13 +14,15 @@ SERRAN_ASSEMBLY="/media/bigvol/peguerin/donnees/serran_genome_lgt3000.fasta"
SERRAN_CHROMIUM_INTERLAVED="/media/bigvol/peguerin/xxx/outs/barcoded.fastq.gz"
## index genome assembly
nohup bwa index $SERRAN_ASSEMBLY &
bwa index $SERRAN_ASSEMBLY
mv nohup.out index.log
## run alignments
nohup bwa mem -t 48 $SERRAN_ASSEMBLY -p $SERRAN_CHROMIUM_INTERLAVED &
bwa mem -t 48 $SERRAN_ASSEMBLY -p $SERRAN_CHROMIUM_INTERLAVED > aln_serran.sam
mv nohup.out aln.log
| samtools view -Sb - | samtools sort -n - ./CHROMIUM-sorted &
samtools view -Sb aln_serran.sam | samtools sort -n -o aln_serran.sorted.bam - &
echo "aln_serran.sorted.bam" > alignments.fof
## Running ARCS...
nohup ./ARCS.sh 5 0.05 30000 $SERRAN_ASSEMBLY &
\ No newline at end of file
./ARCS.sh 5 0.05 30000 $SERRAN_ASSEMBLY
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment