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AliTVTeam / AliTV

Visualize whole genome alignments as linear maps
https://alitvteam.github.io/AliTV/d3/AliTV.html
MIT License
69 stars 11 forks source link

Lastz splitting and filtering #136

Closed mictadlo closed 5 years ago

mictadlo commented 6 years ago

Hi, Is it possible to run lastz separately i.e. could I split my assembly into many parts and align it against the reference genome (chromosome based)? Next, I would like to filter the alignment in order to create for each chromosome a file with mapped contigs to this chromosome.

Thank you in advance.

Michal

iimog commented 6 years ago

Hi Michal, there is the possibility to use pre-computed alignments as input for AliTV. However I'm not sure whether it is possible to split and filter those alignments. Maybe @greatfireball has some idea?

mictadlo commented 6 years ago

Hi @iimog, Could you please provide how to use pre-computed alignments as input for AliTV and how a lastz command should look like so its output would be accepted by AliTV?

Thank you in advance.

Michal

iimog commented 5 years ago

Sorry I never replied. I'm pretty sure this is no longer relevant, still... the documentation is located here: https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/doc/alitv.md#section-alignment

Import of pre-computed alignments can still be tricky (for example identifiers have illegal characters or are duplicated in different genomes). Feel free to open a new issue if you still need this and can not get it working using the docu.