Description

Full-Length Non-Chimeric (FLNC) PacBio Iso-Seq reads were aligned against the D. ananassae DanaRefSeq2 genome assembly using the pbmm2 wrapper for minimap2. The alignments of FLNC reads were analyzed by the TAMA Collapse pipeline to construct the collection of transcript models. The transcript models were then characterized by the TAMA GO Open Reading Frame (ORF) and Nonsense-Mediated Decay (NMD) prediction pipelines.

The PacBio Iso-Seq data were produced by Chinmay P. Rele from the Reed Lab at The University of Alabama.

References

Kuo RI, Cheng Y, Zhang R, Brown JWS, Smith J, Archibald AL, Burt DW. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics. 2020 Oct 30;21(1):751. doi: 10.1186/s12864-020-07123-7.

Li H. New strategies to improve minimap2 alignment accuracy. Bioinformatics. 2021 Oct 8;37(23):4572-4. doi: 10.1093/bioinformatics/btab705.