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Supported data types

Sequencing data

Spl-IsoQuant support all kinds of long RNA data:

  • PacBio CCS
  • ONT dRNA / ONT cDNA
  • Assembled / corrected transcript sequences

Reads must be provided in FASTQ/FASTA format (can be gzipped) or unmapped BAM format.
If you have already aligned your reads to the reference genome, simply provide sorted and indexed BAM files.

Spl-IsoQuant supports the following protocols:

  • 10x 3' v3 single-cell;
  • 10x 3' Visium spatial data;
  • 10x Visium HD;
  • Curio Biosciences spatial data;
  • Stereo-seq spatial data;
  • Any other single-cell or spatial protocol with barcode and UMI sequences (see more about custom molecule description).

Supported reference data

Reference genome should be provided in multi-FASTA format (can be gzipped). The reference genome is mandatory even when BAM files are provided.

Reference gene annotation is also mandatory for single-cell / spatial analysis It should be provided in GFF/GTF format (can be gzipped). It will be converted to gffutils database. Information on converted databases will be stored in your ~/.config/Spl-IsoQuant/db_config.json to increase speed of future runs. You can also provide gffutils database manually. Make sure that chromosome/scaffold names are identical in FASTA file and gene annotation. Note that gffutils databases may not work correctly on NFS shares. It is possible to set a designated folder for the database with --genedb_output (different from the output directory).

Pre-constructed aligner index can also be provided to reduce mapping time.