JupiterPlot
JupiterPlot copied to clipboard
JustinChu
Only a fraction of the represented scaffolds aligned to the reference.
Hi, I have been running JupiterPlot to compare an assembly to a reference genome and ended up with fractions of scaffolds (new assembly) aligning to the reference genome. However, the plot leads to think that whole scaffolds were represented. Is it expected?
Hi,
I'm not entirely sure what you mean. What do you mean by whole scaffolds?
Some scaffolds will be omitted by default if they are too small. You can include them (by adjusting the ng parameter) but after a certain point, it will likely become unwieldy.
Hi, In my case, the first scaffold presented in the figure is ~58Mbp long but only ~14Mb map to chromosome 1 of the reference. It is also the case for most of the other scaffolds.
The figure shows this scaffold that mapped to chromosome 1 without showing the part that wasn't mapping chromosome 1. However, looking into the file "prefix-agp.bed", I can see in the two last columns that this scaffold mapped to chromosome 1 from position ~400 to position ~14000000 (the expected max position would be 58000000).
Is it expected or did I do something wrong?
Julien Prunier, PhD Professionnel de Recherche, Research Associate Université Laval, Laval University 1-581-305-8461
On Thu, Feb 18, 2021 at 11:06 AM Justin Chu [email protected] wrote:
Hi,
I'm not entirely sure what you mean. What do you mean by whole scaffolds?
Some scaffolds will be omitted by default if they are too small. You can include them (by adjusting the ng parameter) but after a certain point, it will likely become unwieldy.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/JustinChu/JupiterPlot/issues/33#issuecomment-781451860, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADVDJWHOCEQDSISPNMHWQYDS7U3KFANCNFSM4X2EXJLQ .
Is this 14Mbp alignment the only alignment to the scaffold? Are you sure there aren't more alignments later on?
The prefix-agp.bed is not the final alignment result considered in the final figure. To make the alignment easier on the aligner and to allow for translocations/misassemblies to be seen more easily, the scaffolds are broken up into scaftigs (i.e. broken at gaps) before alignment. They are then filtered by MAPQ to remove low quality alignments. Later contiguous blocks of alignments are merged together if they are within the maxGap distance. This effectively pastes the contiguous block back together (to the full-length alignment) unless a major translocation occurs between a block.