Does anyone know how to go from a contig file with the scaffolding information in an AGP file to a full scaffolded multifasta file?
Thanks
Thanks
-
-
Hi,
did you solve the problem? right now, I have to solve the same problem. -
If you have contigs with scaffolding info in the agp file -
Than you can pad gaps between the contigs with N's (according to agp file) and write a multifasta file with an entry for each scaffold. Can be done with a bit of perl programming.
(In my case I use newbler output, which includes the scaffolds sequences in the multifasta file).
If you have source reads data, and would like to try a different scaffolder(s) -
have a look at the following review for the scaffolding tools available:
Comment
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM
Comment