RNA-seq Data Handling and Analysis - Department of Statistics and Probability

Bowtie/Tophat/Cufflinks bowtie-build pseudomolecule.fa pseudomolecule.index tophat -p 6 --solexa1.3-quals -i 5 -I 1000 -r 100 --no-novel-juncs --GTF pseudomolecule.gtf -o /output/directory pseudomolecule.index purified_reads.fastq samtools sort tophat ...

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