RagTag results

Question

[synthiiihuh]

Why is there a fixed gap size of 100bp in between the contigs using the RagTag Scaffold option?

Answer 1

[shelkmike]

That's because RagTag doesn't know the exact gap length. Many scaffolders introduce gaps with a fixed length for the same reason.

[synthiiihuh]

Is there any way I could change this gap length using RagTag. Or will this 100bp gap size after every contig would give any erroneous results during annotation

[shelkmike]

If you read the manual of RagTag, you'll see that there is an option -r that makes RagTag to infer gap sizes from reference (https://github.com/malonge/RagTag/wiki/scaffold).
I don't think that gaps of 100 bp will affect the annotation significantly.