Description

This track shows introns supported by the aligned reads. All BAM files for the cells of a cluster were merged and reads with a gap longer than 70 bp and shorter than 500 kbp were retained. These gaps are shown and are annotated with the number of reads, in the 'score' field.

Display Conventions and Configuration

You can use the 'score' filter on the track configuration page to show only introns with a certain number of supporting reads. The maximum number of reads that are shown is 1000, even if more reads support an intron.

Methods

The alignments were used as submitted. All BAM files for all cells of a cluster were merged with "samtools merge". On the resulting merged BAM file the software IntronProspector was run.

Data Access

The original IntronProspector .bed files can be downloaded from the track hub directory. You can also find *.calls.tsv files with more details about each junction, e.g. number of uniquely mapping reads.

Credits

IntronProspector was written by Mark Diekhans.

References

Mark Diekhans, IntronProspector GitHub Repository . Github 2018

The Tabula Muris Consortium, Stephen R. Quake, Tony Wyss-Coray, Spyros DarmanisThe Tabula Muris Consortium, Stephen R. Quake, Tony Wyss-Coray, Spyros Darmanis:
Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris. bioRxiv March 2018, manuscript 237446.