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I have run framefix on a few bacterial hybrid assemblies (ONT+Illumina) generated with Unicycler or Flye/Racon/Pilon. I am using the Uniref90 database:
I have a "Gold Standard" PacBio reference sequence that I am comparing the ONT+Illumina hybrid assemblies to, and when I run NucDiff against my assembly without framefix and then my assembly with framefix, it appears that errors are introduced. For example (Pseudomonas aeruginosa):
Without framefix:
Insertions: 73
Deletions: 28
Substitutions: 5
With framefix
Insertions: 99
Deletions: 57
Substitutions: 5
Do you have any idea why this might be? Should I try a different database?
Thanks!
The text was updated successfully, but these errors were encountered:
Thanks for trying it out. To figure out what is going on, could you post the output_prefix.diamond_nr.txt file? This reports the database sequence matches that were used to adjust each frameshift.
Hi Paul,
I have run framefix on a few bacterial hybrid assemblies (ONT+Illumina) generated with Unicycler or Flye/Racon/Pilon. I am using the Uniref90 database:
/path/to/framefix /path/to/assembly.fasta 1e-25 /path/to/uniref90.dmnd
I have a "Gold Standard" PacBio reference sequence that I am comparing the ONT+Illumina hybrid assemblies to, and when I run NucDiff against my assembly without framefix and then my assembly with framefix, it appears that errors are introduced. For example (Pseudomonas aeruginosa):
Without framefix:
Insertions: 73
Deletions: 28
Substitutions: 5
With framefix
Insertions: 99
Deletions: 57
Substitutions: 5
Do you have any idea why this might be? Should I try a different database?
Thanks!
The text was updated successfully, but these errors were encountered: