Quick start

• Spl-IsoQuant can be downloaded from https://github.com/algbio/spl-IsoQuant:

  git clone https://github.com/algbio/spl-IsoQuant.git
  cd spl-IsoQuant
  pip install -r requirements.txt
  

• If installing manually, you will need Python3 (3.8 or higher), gffutils, pysam, pyfaidx 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:

  splisoquant.py --test
  

• To run Spl-IsoQuant on 10x single-cell data use the following command:

  splisoquant.py --reference /PATH/TO/reference_genome.fasta \
  --genedb /PATH/TO/gene_annotation.gtf --complete_genedb \
  --fastq /PATH/TO/10x.fastq.gz --barcode_whitelist /PATH/TO/barcodes.tsv \
  --barcode2spot /PATH/TO/barcodes_to_celltype.tsv
  --mode tenX_v3 --data_type (pacbio_ccs|nanopore) -o OUTPUT_FOLDER
  

• Or provide your own table with barcoded reads:

  splisoquant.py --reference /PATH/TO/reference_genome.fasta \
  --genedb /PATH/TO/gene_annotation.gtf --complete_genedb \
  --fastq /PATH/TO/10x.fastq.gz --barcoded_reads /PATH/TO/barcoded_reads.tsv \
  --barcode2spot /PATH/TO/barcodes_to_celltype.tsv
  --mode tenX_v3 --data_type (pacbio_ccs|nanopore) -o OUTPUT_FOLDER
  

• For example, using the toy Stereo-seq data provided within this repository:

  ./splisoquant.py --data_type nanopore --mode stereoseq_nosplit  \
  --fastq /home/andreyp/ablab/spl-IsoQuant/tests/stereo/S1.4K.subsample.fq.gz \
  --barcode_whitelist /home/andreyp/ablab/spl-IsoQuant/tests/stereo/barcodes.tsv \
  --reference /home/andreyp/ablab/spl-IsoQuant/tests/stereo/GRCm39.chrX.7.fa.gz \
  --genedb /home/andreyp/ablab/spl-IsoQuant/tests/stereo/gencode.chrX.ENSMUSG00000031153.gtf \
  --complete_genedb --output splisoquant_test  -p TEST_DATA
  

• You can also define your own molecule structure using the molecule description format (MDF) and provided to Spl-IsoQuant via --molecule option:

  splisoquant.py --reference /PATH/TO/reference_genome.fasta \
  --genedb /PATH/TO/gene_annotation.gtf --complete_genedb \
  --fastq /PATH/TO/10x.fastq.gz --molecule /PATH/TO/my_protocol.mdf \
  --mode custom_sc --data_type (pacbio_ccs|nanopore) -o OUTPUT_FOLDER