Commit a320236a authored by Holger Brandl's avatar Holger Brandl

reduced bootstrapping for kallisto

parent 4c7b1efa
......@@ -440,7 +440,7 @@ for fastqFile in ${fastqFiles}; do
# jl submit -t 5 "kallisto quant -i ${KALLI} -o ${OUTDIR} --pseudobam --single -l 200 -s 20 -b 50 ${fastqFile} > ${OUTDIR}/out.sam"
# jl submit -t 5 "kallisto quant -t 5 -i ${KALLI} -o $(basename ${fastqFile} .fastq.gz) --single -l 200 -s 20 -b 50 ${fastqFile}"
# jl submit -t 5 "kallisto quant -i ${KALLI} -o ${OUTDIR} --pseudobam --single -l 200 -s 20 -b 50 ${fastqFile} > ${OUTDIR}/out.sam && samtools view -Sb ${OUTDIR}/out.sam > ${OUTDIR}/out.bam"
jl submit --jl .isoex -n kallisto_${fastqBase} -t 5 "kallisto quant -t 5 -i ${KALLISTO_INDEX} -o ${fastqBase} --single -l 200 -s 20 -b 50 ${fastqFile} &> ${fastqBase}/kallisto.log"
jl submit --jl .isoex -n kallisto_${fastqBase} -t 5 "kallisto quant -t 5 -i ${KALLISTO_INDEX} -o ${fastqBase} --single -l 200 -s 20 -b 25 ${fastqFile} &> ${fastqBase}/kallisto.log"
done
jl wait
......
Markdown is supported
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