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RSEM transcript alignment

RSEM homepage:

RSEM paper:

prepare-reference help:

calculate-expression help:

RSEM expects a GTF file with only exons, which are each assigned to a transcript_id.

Note that we only align to chromosome 1 for demonstration purposes.

awk '$3 == "exon"' gtf/Homo_sapiens.GRCh38.79.chrom1.gtf > gtf/Homo_sapiens.GRCh38.79.chrom1.exons.gtf

RSEM will then prepare a reference transcriptome against which to align reads.

mkdir rsemGenome
rsem-prepare-reference --gtf gtf/Homo_sapiens.GRCh38.79.chrom1.exons.gtf genome/Homo_sapiens.GRCh38.dna.chromosome.1.fa rsemGenome/GRCh38.79.chrom1
rsem-calculate-expression -p 12 --paired-end fastq/SRR1039508_1.fastq fastq/SRR1039508_2.fastq rsemGenome/GRCh38.79.chrom1 SRR1039508