【RSEMの使い方】RNA-Seq解析における遺伝子発現量の定量

$ conda install -c bioconda rsem

$ rsem-prepare-reference -h

NAME rsem-prepare-reference - Prepare transcript references for RSEM and optionally build BOWTIE/BOWTIE2/STAR/HISAT2(transcriptome) indices. SYNOPSIS rsem-prepare-reference [options] reference_fasta_file(s) reference_name ARGUMENTS reference_fasta_file(s) Either a comma-separated list of Multi-FASTA formatted files OR a directory name. If a directory name is specified, RSEM will read all files with suffix ".fa" or ".fasta" in this directory. The files should contain either the sequences of transcripts or an entire genome, depending on whether the '--gtf' option is used. ... ...

$ rsem-prepare-reference --gtf annotation.gtf --hisat2-hca --hisat2-path [hisat2へのパス] reference.fa index/reference

$ rsem-calculate-expression --hisat2-hca --hisat2-path [hisat2へのパス] --paired-end read_1.fastq.gz read_2.fastq.gz index/reference sample1

$ rsem-generate-data-matrix sample1.genes.results sample2.genes.results sample3.genes.results sample4.genes.results > all.genes.results $ rsem-generate-data-matrix sample1.isoforms.results sample2.isoforms.results sample3.isoforms.results sample4.isoforms.results > all.isoforms.results