Generating a dotplot following ragtag scaffolding
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3 months ago
kschach2 • 0

Hello,

I recently used ragtag to correct de novo assembled contigs and order and orient them to the pig reference genome using ragtag scaffold. I'd like to generate dotplots to assess the assembly. I've read a couple posts where people have suggested using mummerplot to do this; however, I cannot figure out how to use the output files from the ragtag scaffold command to generate these plots using mummerplot. I've tried using the query_against_ref.paf and ragtag.scaffolds.agp files as input for mummerplot, which produced the following error:

ERROR: Could not read ragtag.scaffolds.agp, Unrecognized file type


I also tried to use these files as input for show-tiling, which produced the following error:

ERROR: Could not parse delta file, ragtag.scaffolds.stats
error no: 400


Does anyone have any advice on how to use ragtag scaffold output files to generate dotplots using mummerplot?

Thanks!

ragtag dotplot mummerplot genome assembly • 263 views
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Entering edit mode

The output from ragtag, that you want, is just the fasta file containing the scaffolded genome. You need to then align this to the reference using nucmer (from MUMmer), to generate the delta file. This delta file is the alignment file you can then use to generate a dotplot (after some processing, i think you would wabt to filter with delta-filter and then convert to coordinates with show-coords) or for show-tiling

Try use dgenies as well. It might be quicker to get a nice dotplot.