Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Why BUSCO reports fewer genes after RaGOO?

See original GitHub issue

Hey there! I used: python3 ragoo.py contigs.fasta reference.fasta Then, surprisingly BUSCO reported fewer genes after RaGOO (Table). One complete gene and 4 fragmented genes lost 😦 . Table.

Genes         Contigs  Contigs&RaGOO
Complete sing    4380           4379
Complete dupl       7              7
Fragmented         13              9
Missing            15             20

Is that because of contig orienting & ordering? Or another reason? How to set RaGOO parameters to save these genes? Thanks in advance!

Cheers, Ural

Issue Analytics

State:
Created 3 years ago
Comments:5 (2 by maintainers)

Top GitHub Comments

2reactions

mschatzcommented, May 27, 2020

Yes, Ive noticed this too that the BUSCO output is not completely stable in that reordering the contigs in a fasta file (but not changing the sequence at all) can change the scores a bit. I dont have a deep understanding of it other than there must be some heuristics involved that are sensitive to how the data are internally batched

Mike

On Wed, May 27, 2020 at 11:28 AM Michael Alonge notifications@github.com wrote:

Closed #66 https://github.com/malonge/RaGOO/issues/66.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/malonge/RaGOO/issues/66#event-3378733485, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABP344OWRH2DW6L7UUXND3RTUWTTANCNFSM4NET4TLQ .

0reactions

Ural-Yunusbaevcommented, May 28, 2020

Thank you!

Top Results From Across the Web

RaGOO: fast and accurate reference-guided scaffolding of ...

Here, we introduce RaGOO, an open-source method which utilizes Minimap2 [24] alignments to a closely related reference genome to quickly ...

BUSCO Update: Novel and Streamlined Workflows along with ...

A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable ...

Towards complete and error-free genome assemblies of all ...

After we applied these tools, the primary assembly sizes and the k-mer and BUSCO gene duplication rates were all reduced, and their correlations ......

The changing face of genome assemblies: Guidance on ...

Elevated levels of BUSCO duplicates may alternatively report a contribution of whole genome duplication to the lineage, as is particularly ...

Whole genome assembly and annotation of the lucerne weevil ...

(BUSCO) scores are above 96% for single-copy orthologs derived from eukaryotes, ... fewer than those reported in other coleopteran genomes, ...