Description

This track contains read alignments, polyA sites and merged transcript models obtained in the GENCODE Capture Long-Seq (CLS) project, phase 1.

The merged transcript models were obtained by merging aligned PacBio reads with compatible intron/exon structures using compmerge with two distinct procedures, anchored and non-anchored. Briefly,

• The anchored approach prevents the transcripts whose end(s) are supported by CAGE or polyA data from being merged into a longer, compatible transcript "container". This preserves all supported transcript ends in the output, including "internal" sites.
• Conversely, with the non-anchored method, all transcripts with compatible intron chains are merged into a single container, regardless of their end support, similarly to e.g. Cuffmerge.

All merged transcript models are derived from aligned PacBio reads with the following properties:

• If spliced, all their introns must be canonical (GT|GC / AG).
• If monoexonic, they must bear a detectable polyA tail.

See Lagarde et al. for more details.

Credits

This data was produced as part of the GENCODE project, with funding from the National Human Genome Research Institute (NHGRI).

For inquiries, please contact:
Julien Lagarde (CRG, Barcelona, Spain, julienlag AT gmail.com)
Rory Johnson (University of Bern, Switzerland, rory.johnson AT dkf.unibe.ch)
Roderic Guigo (CRG, Barcelona, Spain, roderic.guigo AT crg.cat)

References

Supplementary data can be accessed through the CLS portal.

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS). Julien Lagarde, Barbara Uszczynska-Ratajczak, Silvia Carbonell, Carrie Davis, Thomas R Gingeras, Adam Frankish, Jennifer Harrow, Roderic Guigo, Rory Johnson. doi: https://doi.org/10.1101/105064.