pipelines-docs

Transcript Quantification

The pipeline uses RSEM (RNA-Seq by Expectation Maximization) to quantify gene and isoform abundances from RNA-seq data. It accepts alignments to the reference transcriptome generated by STAR.

Quantifying Transcript Abundance

Transcript abundance quantification

rsem-calculate-expression \
    --fragment-length-max 1000 \
    --no-bam-output \
    --paired-end \
    --estimate-rspd \
    --calc-ci \
    --forward-prob 0.0 \
    --bam transcriptome.bam \
    rsem_reference \
    OUT

Note: The above command assumes a paired-end, RF/fr-firststrand stranded protocol. The RSEM reference was generated using a slightly modified version of the reference genome that excludes ALT, HLA and Decoy contigs. Please refer to the reference files section for further details.

Implementation with RSEM

The pipeline implements RSEM version v1.3.3. The software call is executed through a Python wrapper.

Source Code

All the relevant code can be accessed in the GitHub repository:

• run_RSEM.py^₁ [RSEM]

_{1: Original author: Francois Aguet}

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