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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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Failure to Map #83

Open YianniL opened 6 years ago

YianniL commented 6 years ago

Hi,

I'm really interested in using graphmap for doing some Nanopore alignments with predicted sequences but I can not seem to get an alignment. I tried to get an alignment with a simple sequence just to test it out, but I am not successful. For example:

Say I have dog.fasta like this: >dog ATC

And ref.fasta like this: >dog ATCG

I am getting 0 mapped reads. Even when I try to align ref.fasta to itself I am getting 0 mapped reads. This is the command I'm running:

graphmap align -r ref.fasta -d dog.fasta -o output.sam

Any help would be greatly appreciated because we really want to use graphmap for our alignments. Thanks for your time!

Best, YianniL

ghost commented 6 years ago

It might be that your sequences are just too short and the algorithm does not find any seeds (anchors?) to do the alignment. Make the example a bit longer about 20 to 30 nt... Hope I am right with this. Don't know the algo. in detail.