Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)

Simulated ONT and PacBio RNA-Seq data for "Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns" paper (Mikheenko et al., Genome Research, 2022). All details can be found in the Methods section of the paper.

PacBio.simulated_uniform_coverage.fasta.gz and ONT.simulated_uniform_coverage.fasta.gz files were used in Supplemental Note “Benchmarking of the read-to-isoform assignment algorithm”.

ONT.simulated_real_expression.fasta.gz file and all GTF files were used in the Section "Splice site correction improves transcript discovery precision". mouse.gencode.M26.spatial.15percent.reduced.gtf was used as the annotation file for all tools. mouse.gencode.M26.spatial.15percent.expressed.gtf contains the set of all expressed isoforms. mouse.gencode.M26.spatial.15percent.expressed_kept.gtf contains those of the isoforms that are in presented in the annotation file ("known" transcripts), mouse.gencode.M26.spatial.15percent.reduced.gtf contains expressed isoforms that were removed from the annotation ("novel" transcripts).