10x Genomics
Chromium Genome & Exome

Long Ranger2.1, printed on 11/14/2024

Linked-Reads: Reads and Molecules

THe LINKED-READ view shows a selection of the reads in a given interval. Each dot corresponds to a read and loupe draws a thin line between reads from the same GEM. Reads from the same GEM are also horizontally aligned but Loupe may place multiple molecule on the same horizontal position if they do not overlap.

Loupe separates molecules by the haplotypes that LONG-RANGER assigned to them. Loupe places one haplotype on the top and the second haplotype in the middle. Unphased molecules are placed at the bottom.

The LINKED-READ view support two modes.

• In Haplotype discrimination mode (the default), the different haplotypes (as well as unphased molecules) are colored from different color palettes.

• In Lariat mode, Loupe colors reads based on their alignment properties:
  • Reads with a MAPQ less than 30 are colored grey
  • Reads with a high mapq that uniquely aligned are colored black
  • Reads with a high mapq that lariat was able to align because of their linkage to other reads are colored green.