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MariaNattestad / Assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
http://assemblytics.com
MIT License
135 stars 28 forks source link

delta files problem #60

Closed Gon1976 closed 4 months ago

Gon1976 commented 6 months ago

Open new issue.

I dont really make changes to the output of nucmer. I run as assemblytics webpage indicates: nucmer --maxmatch -l 100 -c 500 TcDm25_H1.fasta Dm28c_v4.fasta -p Dm28vsH1 and upload without changes to assemblytics. Do you think could be a problem with my fasta files or my nucmer installation?

Your answer was: "I'm guessing you tried to change the file programmatically and accidentally added some newlines where they shouldn't be. When you fix this, please take a close look at your file in a text editor and also try running it through the MUMmer tool suite first before reporting problems in Assemblytics, since it will be faster for you to check that these files are valid using e.g. MUMmer's "show-aligns" or "coords" commands. Once those are working and it looks okay , then you can try Assemblytics again. Good luck!"

MariaNattestad commented 6 months ago

Did the show-aligns and coords commands work?

Gon1976 commented 6 months ago

I dont understand how works show-aligns deltafile refID qyID (refID and qyID refers to chromosomes names? )

MariaNattestad commented 6 months ago

Check the MUMmer documentation for that one.

On Fri, Mar 15, 2024 at 7:06 AM Gon1976 @.***> wrote:

I dont understand how works show-aligns deltafile refID qyID (refID and qyID refers to chromosomes names? )

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