This is a test version of Biostars. For the public version, visit https://www.biostars.org.
RagTag results

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

ngs scaffolding ragtag gaps
• 1,262 views • link
updated by shelkmike shelkmike • written by synthiiihuh • synthiiihuh

1 answer

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

• 0 views • link
written by shelkmike shelkmike

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

• 0 views • link
written by synthiiihuh • synthiiihuh

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.

• 0 views • link
written by shelkmike shelkmike

Log in to answer this question.

More posts like this