Question about vg giraffe, vg surject and Visualization tool for mapping result

Question

[gulin]

I have two questions about vg giraffe mapping.

1. How does vg surject function work? Is it doing another alignment against the linear reference after vg giraffe. I have receive warnings: Refusing to perform very large alignment against 114514 bp strand split graph for read. I am worried that I will lose some important information(e.g. SV) in GAM file.

2. Is there any visualization tool for giraffe mapping result? I want to discover where my read actually aligned to.

   I am looking forward to your reply!Thanks!

Answer 1

[Jordan M Eizenga]

vg surject doesn't do a full realignment of the read against the linear reference. In general, it tries to preserve as much of the graph alignment as possible and only realigns between the portions of the alignment that overlap the linear reference. Sometimes, a short alignment in the graph can correspond to a very long alignment in the linear reference (e.g. over a long deletion), which can lead to those warnings.

The space of visualization tools for graph alignments is unfortunately not so mature yet. The most capable tool is probably sequenceTubeMap, but (as of the last time I checked) it's somewhat involved to get started with.