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calkan / sonic

Some Organism's Nucleotide Information Container
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creation of sonic file in other orgs #15

Open pbreeder opened 2 years ago

pbreeder commented 2 years ago

Hi all,

I would like to test the Valor2 program in the plant (hazelnut pacbio data). But sonic file and others need to be created. My question is, is it possible to do SV analysis on the plant for this program, if so, is there a way to do it without creating a sonic file?

thanks

calkan commented 2 years ago

hi

VALOR uses sonic files to retrieve genome metadata (gaps, dups, gc content, repeats), which is in turn used to reduce false positives. You will still need to create one, but if you dont have access to gaps,dups,repeats, you can pass empty files. Only the GC content will be calculated using the assembly fasta file. But again, lack of gaps/dups/repeats will increase false calls.

pbreeder commented 2 years ago

Dear Alkan,

Firstly, thank you very much for your kind interest. As you mentioned about metadata, I created the empty files (gaps, dups, gc content, repeats) and sonic file was created by sonic. Than, valor was used for detection of svs from pacbio reads. Thus, empty sv files were created the end of the run. I could not notice this issue.

Thank you, My best regards

calkan commented 2 years ago

VALOR does not work with PacBio reads - it is a linked-read caller (i.e., 10X Genomics data). To call SVs using PacBio data, try sniffles instead (https://github.com/fritzsedlazeck/Sniffles)

pbreeder commented 2 years ago

Thank you very much, for your patients