Commit fe845d7d authored by peguerin's avatar peguerin
Browse files

index genome

parent fb67be9f
......@@ -2,3 +2,25 @@
## produce interleaved filefastq from 10X raw data
longranger basic --fastqs=/media/bigvol/peguerin/donnees/lib10x/ --id=xxx --sample=Lib_10
cd ~/arcs/Examples/serran
mkdir ../serran
cp *sh ../serran
cp *py ../serran/
cd ../serran/
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 &
## run alignments
nohup bwa mem -t 48 $SERRAN_ASSEMBLY -p $SERRAN_CHROMIUM_INTERLAVED &
| samtools view -Sb - | samtools sort -n - ./CHROMIUM-sorted &
## Running ARCS...
nohup ./ARCS.sh 5 0.05 30000 $SERRAN_ASSEMBLY &
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