Multi-Platform Analysis and Quantification of Transcripts
Please consult the Installation Guide page for detailed installation instructions.
The first step in the MPAQT pipeline involves creating an index for your transcriptome and its annotation. For this demonstration, we'll utilize the latest GENCODE transcriptome and annotation:
| Data | Format | Name | Link |
|---|---|---|---|
| Transcriptome | FASTA | gencode.v46.transcripts.fa.gz |
Download |
| Annotation | GTF | gencode.v46.annotation.gtf.gz |
Download |
To generate the index, execute the following command:
mpaqt index \\
--ref_txome references/gencode.v46.transcripts.fa \\
--ref_annot references/gencode.v46.annotation.gtf \\
--output references/gencode.v46.index
MPAQT ————— Generating index
——————————— Generating kallisto index for reference transcriptome.
——————————— Generating P matrix
——————————— Generating covariance matrix
——————————— Finalizing MPAQT index
——————————— Index is generated successfully and stored in references/gencode.v46.index.mpaqt
This command produces two indices for analysis:
gencode.v46.index.**mpaqt**, tailored for the MPAQT quantification framework.gencode.v46.index.**kallisto**, designed for preprocessing short-read RNA-seq with the kallisto bus tool.<aside>
💡 The MPAQT index for GENCODE v46 has already been generated and is available in the references directory of the GitHub repository as gencode.v46.index.mpaqt. If you prefer to skip the index generation and use this file, you will need to create the kallisto index using the following command:
kallisto index \\
--index references/gencode.v46.index.**kallisto** \\
references/gencode.v46.transcripts.fa
</aside>
Although index creation may take some time, it's a one-time task for a transcriptome and annotation pair, offering repeated utilization for future analyses.
The subsequent step involves creating a project with a specified index. Samples added to this project will undergo analysis using the designated index. For instance, let's establish a project named neurondiff using the gencode.v46.index.mpaqt generated in the previous step:
mpaqt create project \\
--index references/gencode.v46.index.mpaqt \\
neurondiff
MPAQT ————— Creating project
——————————— Project neurondiff has been created in MPAQT/projects/neurondiff.