Closed SuPrSh closed 3 years ago
Hi there,
This is showing that there is a component in your AGP file (k141_114310
) that is not in the assembly. In other words, that AGP file defines a scaffolding solution for some other assembly, not ragtag.ggan.scaffold.fasta
. In order for RagTag "merge" to work, all AGP files must contain the exact same set of components as the assembly. Read here for more details.
I would like to revisit this comment. I have a similar situation in that when scaffolding, SALSA2 corrected 8 of my contigs and broke them into 2. Thus, a contig that appears as ctg927 in the .fasta file appears as ctg927_1 and ctg927_2 in the resulting AGP file.
In this situation, would you advise to polish the preliminary assembly before scaffolding?
Thanks!
Hello, I am getting constant error while using merge command in ragtag