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eth-sri / astarix

AStarix: Fast and Optimal Sequence-to-Graph Aligner
Mozilla Public License 2.0
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RNAseq #2

Open jdmontenegro opened 3 years ago

jdmontenegro commented 3 years ago

Hi,

First of all, thank you for such an interesting tool. I am really interesed in using it in the near future. One question though, how suitable would this tool be for mapping RNA-seq reads to a diploid reference graph? If this has been adressed before, please let me know where to look for correct parameters, if this is an interesting case scenario, that would require some development, I would be more than happy to help.

Best regards,

Juan D. Montenegro

pesho-ivanov commented 3 years ago

Dear Juan,

Thank you for the offering your help. The current state of the tool is experimental and lacks some production features (e.g. file format support, memory optimization, scaling to human genome sizes). Nevertheless, I am working in the direction of bringing optimality guarantees to practice.

Regarding RNA-seq, AStarix has not been tested on non-simulated data yes and does not handle RNA in a special way (e.g. splicing junctions are not modeled) so I would not expect great results.

I will update this thread once the tool is ready to be tested on real data.

Best, Pesho