Mosaik Reference-based Assembly of Paired-End Run Problems

[Robert Leach]

Hi,

I'm having trouble viewing the arcs from mate pairs assembled using Mosaik.  I know there's mate pairs present because of the verbose output from the mosaik assembler:

                                original             resolved   
----------------------------------------------------------------
# orphaned:               21123432 (13.2 %)    13220407 ( 8.3 %)
# both mates unique:      75994117 (47.6 %)    73475629 (46.0 %)
# one mate non-unique:    22719097 (14.2 %)    14821859 ( 9.3 %)
# both mates non-unique:  39902833 (25.0 %)           0 ( 0.0 %)
----------------------------------------------------------------
total:                   159739479            101517895 (63.6 %)

Chromosomes 1 & 2 have the most reads mapped to them, but I've been scrolling through the chromosome at a resolution which says arcs are drawn, but cannot find any.  When I view with the display mode set to standard or variants, I can see the mapped reads, but when I switch to mate_pairs, I can't find anything.  Is there an incompatibility with Mosaik or could I have screwed something up in the assembly?  There are no errors from Mosaik at any of the steps I performed.  How should I debug this issue?

Thanks,

Rob

Robert W. Leach
Scientific Programmer
Center for Computational Research
Center of Excellence in Bioinformatics
University at Buffalo
http://www.ccr.buffalo.edu/
Work: 881-7516

[Marc Fiume]

Hi Robert, 

Mate pair mode relies on the records in your BAM file to contain correct matepair information. One way to check if your BAM file contains correct matepair information is to open up the Table View in Savant and look at the values in the "Mate Position" field. They should be nonzero.

If your data is indeed paired, I would suggest running samtools fixmate on your file, which fills in matepair information needed by Savant. 

Let me know if this helps, if not, I'd be happy to look at this further. 

Hope you enjoy Savant! 
Marc