leoisl
commented
1 year ago General stats
Gene: cpe003_contig_3_00225
- nb of reads minimap2 mapped to
cpe003_contig_3_00225: 1605- Note: pandora mapped reads to ~200k genes, while minimap2 mapped reads just to this gene. Although this comparison is not fair, I think this is the closest to the true number of reads that should map to this gene. minimap2 also should be able to map most of these reads to
cpe003_contig_3_00225even if we mapped to the whole plasmid instead, if not all of them, given that it can multimap reads;
- Note: pandora mapped reads to ~200k genes, while minimap2 mapped reads just to this gene. Although this comparison is not fair, I think this is the closest to the true number of reads that should map to this gene. minimap2 also should be able to map most of these reads to
- nb of reads pandora mapped to
cpe003_contig_3_00225: 718 - nb of reads pandora mapped to other genes: 822
nb_of_reads gene 1 NZ_AP023221.1_00079.fa.msa 265 NZ_CP020848.1_00225.fa.msa 556 NZ_CP020848.1_00226.fa.msa - nb of reads pandora did not map at all: 65
- nb of reads pandora manages to map to
cpe003_contig_3_00225if the PanRG is composed only of this gene: 1539 (718 that we can map with both PanRGs + 821 that mapped to other genes)
Conclusion
This data shows that pandora is able to map almost the same number of reads that minimap2 maps to cpe003_contig_3_00225 (minimap2 can map 1605 reads, pandora can map 1539 reads, a loss of 4% reads, which is totally acceptable IMO and likely due to lower density of minimising kmers on the edges). So there is no significant problem with pandora mapping algorithm or parameters. The main issue is that we don't handle multimapping in pandora. 822 of the 1539 reads pandora can map to cpe003_contig_3_00225 end up being mapped to 3 other genes because they map slightly better there. Solution is to implement multimapping in pandora.
iqbal-lab
This is happening with one of our roundhound runs, but in general we know pandora undermaps reads to the PRGs. In some cases, heavy undermapping happens and this impacts genotyping. This is a breaking issue for roundhound and in this issue we will discuss some things about it and try to solve it.
In one of our plasmid genes,
minimap2maps 1605 reads whilepandoramaps only 718. All reads thatpandoramapsminimap2also maps. I will thus extract the unmapped reads and debug why.This relates to https://github.com/rmcolq/pandora/issues/316 . Although reads undemap more in the edge of genes, we can find undermapping throughout the whole gene