Description

This track represents the alignments of the PacBio IsoSeq data against the individual assemblies of the T2T Marmoset project. These IsoSeq alignments were used for annotation of novel isoforms and novel genes.

Display Conventions and Configuration

This track follows the display conventions for bam alignment tracks. More information about each transcript can be found by clicking on the specific transcript model.

Methods

This tracks displays alignments generated by using minimap2 to map PacBio IsoSeq long reads to the marmoset genome assemblies.

• minimap2

  IsoSeq fastq files were mapped with Minimap2 with parameters -ax splice:hq -uf -t 28. This allows to generate splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome.

Credits

This track was provided by Prajna Hebbar <pnhebbar@ucsc.edu> of UC Santa Cruz.

References

• Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100
• Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574
• Mao, Yafei et al. (2024). Structurally divergent and recurrently mutated regions of primate genomes. Cell, 37:4572-4574