Quick start

• IsoQuant can be downloaded from https://github.com/ablab/IsoQuant or installed via conda:

  conda create -c conda-forge -c bioconda -n isoquant python=3.8 isoquant
  

• If installing manually, you will need Python3 (3.8 or higher), gffutils, pysam, pybedtools, biopython and some other common Python libraries to be installed. See requirements.txt for details. You will also need to have minimap2 and samtools to be in your $PATH variable.

• Verify your installation by running:

  isoquant.py --test
  

• To run IsoQuant on raw FASTQ/FASTA files use the following command

  isoquant.py --reference /PATH/TO/reference_genome.fasta \
  --genedb /PATH/TO/gene_annotation.gtf \
  --fastq /PATH/TO/sample1.fastq.gz /PATH/TO/sample2.fastq.gz \
  --data_type (assembly|pacbio_ccs|nanopore) -o OUTPUT_FOLDER
  

  For example, using the toy data provided within this repository,

  ./isoquant.py --reference tests/toy_data/MAPT.Mouse.reference.fasta \
  --genedb tests/toy_data/MAPT.Mouse.genedb.gtf \
  --fastq tests/toy_data/MAPT.Mouse.ONT.simulated.fastq \
  --data_type nanopore -o toy_data_out
  

• To run IsoQuant on aligned reads (make sure your BAM is sorted and indexed) use the following command:

  isoquant.py --reference /PATH/TO/reference_genome.fasta \
  --genedb /PATH/TO/gene_annotation.gtf \
  --bam /PATH/TO/sample1.sorted.bam /PATH/TO/sample2.sorted.bam \
  --data_type (assembly|pacbio_ccs|nanopore) -o OUTPUT_FOLDER
  

  For example, using the toy data provided within this repository,

  ./isoquant.py --reference tests/toy_data/MAPT.Mouse.reference.fasta \
  --genedb tests/toy_data/MAPT.Mouse.genedb.gtf \
  --fastq tests/toy_data/MAPT.Mouse.ONT.simulated.fastq \
  --data_type nanopore -o toy_data_out
  

• If using official annotations containing gene and transcript features use --complete_genedb to save time.

• Using reference annotation is optional since version 3.0, you may preform de novo transcript discovery without providing --genedb option':

  isoquant.py --reference /PATH/TO/reference_genome.fasta \
  --fastq /PATH/TO/sample1.fastq.gz /PATH/TO/sample2.fastq.gz \
  --data_type (assembly|pacbio|nanopore) -o OUTPUT_FOLDER
  

• If multiple files are provided, IsoQuant will create a single output annotation and a single set of gene/transcript expression tables.