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BMILAB / movAPA

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Is it possible to use use Biostrings AAStringsSet intsed of BSgenome as reference genome object #1

Open HegedusB opened 3 years ago

HegedusB commented 3 years ago

Dear authors, I found your package really useful in my research project. My only problem is that my organisms genome sequence is not available in BSgenome format, only in typical fasta format. Can you give me an advice, how can I use it with you package. Is it really necessary to make a BSgenome version of the genome or there are other, easier ways. Thanks for your help. Cheers, Botond

BMILAB commented 3 years ago

Dear authors, I found your package really useful in my research project. My only problem is that my organisms genome sequence is not available in BSgenome format, only in typical fasta format. Can you give me an advice, how can I use it with you package. Is it really necessary to make a BSgenome version of the genome or there are other, easier ways. Thanks for your help. Cheers, Botond

Hi Botond,

Sorry for the late response, I just found the question you raised long ago. I hope you have solved the problem.

In your case, you should make a BSgenome package by yourself. It is easy to follow the BSgenome help document to make a package of your reference genome. Actually for the "rice demo" we provided in our package, the rice reference genome is also not available in BSgenome, we made it ourselves.

Best,

Wu

HegedusB commented 3 years ago

Hi Wu,

Thanks for the response. I figured out how to transform the genome sequence fasta file into BSgenome format. It was not really hard luckily. Now I am trying to understand the package. Do you mind if I ask questions here if I get stuck?

Best, Botond