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RNAseq_Variant_Calling
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LUYAO REN 6 years ago
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STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix OnePass_ STAR --genomeDir ${SAref_dir} --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix OnePass_


STAR --runMode genomeGenerate --genomeDir　./ --genomeFastaFiles ${STref_dir}/${fasta} --sjdbFileChrStartEnd OnePass_SJ.out.tab --sjdbOverhang 75 --runThreadN 12
STAR --runMode genomeGenerate --genomeDir "./" --genomeFastaFiles ${STref_dir}/${fasta} --sjdbFileChrStartEnd OnePass_SJ.out.tab --sjdbOverhang 75 --runThreadN 12




STAR --genomeDir ./ --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_
STAR --genomeDir "./" --readFilesIn ${fastq_1} ${fastq_2} --readFilesCommand zcat --runThreadN 20 --outFileNamePrefix ${sample}_
>>> >>>


runtime { runtime {

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