I'm trying to use the gap_fill_status.txt file and the liftOverTable to figure out which of my original scaffolds were joined after gap filling.
I've found that in gap_fill_status.txt, the same end of a scaffold will be reported as being being joined to multiple other scaffolds (at least in the way that I am interpreting the file)
The 5' end of ref0003806 has a gap between multiple other scaffolds that is listed as "filled"
When I check in the liftOverTable, it looks like it was joined with ref0002030e5 in the final output.
["ref0002030e5_ref0003806e5", "-", 2413]
I'm happy to just use the liftOverTable to solve this problem, if that is the correct solution, but I'm curious about what happened to the filled gaps between ref0003806e5_ref0003939e3, etc. Perhaps I'm just interpreting the file wrong?
Thanks!
Lisl
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When there are multiple gaps that are filed, PBJelly chooses the one with the higher-quality support. For example, if Gap A-B has 1 read supporting where Gap A-C has 5, we choose to fill A-C and connect those scaffolds.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I'm trying to use the gap_fill_status.txt file and the liftOverTable to figure out which of my original scaffolds were joined after gap filling.
I've found that in gap_fill_status.txt, the same end of a scaffold will be reported as being being joined to multiple other scaffolds (at least in the way that I am interpreting the file)
For example:
ref0002030e5_ref0003806e5 filled
ref0003806e5_ref0003939e3 filled
ref0001191e3_ref0003806e5 filled
The 5' end of ref0003806 has a gap between multiple other scaffolds that is listed as "filled"
When I check in the liftOverTable, it looks like it was joined with ref0002030e5 in the final output.
["ref0002030e5_ref0003806e5", "-", 2413]
I'm happy to just use the liftOverTable to solve this problem, if that is the correct solution, but I'm curious about what happened to the filled gaps between ref0003806e5_ref0003939e3, etc. Perhaps I'm just interpreting the file wrong?
Thanks!
Lisl
When there are multiple gaps that are filed, PBJelly chooses the one with the higher-quality support. For example, if Gap A-B has 1 read supporting where Gap A-C has 5, we choose to fill A-C and connect those scaffolds.