Question: How to generate AGP format using contigs and scaffolds
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gravatar for Prakki Rama
5.0 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

Hi all,

The scaffolds I work on were generated using transcriptome data by L_RNA_Scaffolder. But, I want to know how the scaffolding was done by generating an AGP output (helpful in NCBI submission too). We can try to aligning the contigs on to the scaffolds but my worry is, there is chance of error creeping in. Thanks in advance.

 

 

agp scaffold latest ncbi • 4.0k views
ADD COMMENTlink modified 5.0 years ago by ####210 • written 5.0 years ago by Prakki Rama2.4k
0
gravatar for ####
5.0 years ago by
####210
####210 wrote:

This might help you.

It is a perl program , just run the code and you will get three output file .agp scaffold.fasta, contigs.fasta

Hope this will help

ADD COMMENTlink modified 2.5 years ago by Ram32k • written 5.0 years ago by ####210

Thank you very much. Already found a script from velvet software.

ADD REPLYlink written 5.0 years ago by Prakki Rama2.4k
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