Closed winni2k closed 5 years ago
For a repeat of length L you need a read of length L+2 to pair input and output edges. The shortest repeat in a k=3 graph is 3bp, so you need a read of 5bp covering it to generate links across it. Adding a base at the beginning should generate four links:
>0
GCGTT
>1
CCGTA
Thanks! That works.
A second question, since we're on this topic: Does mccortex annotate links in through bubbles or does mccortex only annotate through cycles? If not, why not?
Links are only added to tangles -- parts of the graph that collapse down then split out again. A simple bubble can be traversed without links if you try walking down all the options one at a time. I'll try to add some better documentation on links - sorry I don't have time right now. The paper on Linked de Bruijn graphs (or my thesis when I upload it) might be the best place to start.
That's a really succinct description! Thank you so much.
On Tue, Oct 16, 2018 at 6:18 PM Isaac Turner notifications@github.com wrote:
Links are only added to tangles -- parts of the graph that collapse down then split out again. A simple bubble can be traversed without links if you try walking down all the options one at a time. I'll try to add some better documentation on links - sorry I don't have time right now. The paper on Linked de Bruijn graphs https://academic.oup.com/bioinformatics/article/34/15/2556/4938484 (or my thesis when I upload it) might be the best place to start.
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I have created a gist with the relevant input and log files.
When I run mccortex with kmer size 3 with an input fasta containing two reads of length 4, and I then thread the same reads through the resulting graph, I do not get any links in the links file. Is this a bug, or am I doing something wrong?