Software  ›   visualization
If your question is not answered here, please email us at:  support@10xgenomics.com

10x Genomics
Chromium Genome & Exome

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.