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gamcil / cblaster

Find clustered hits from a BLAST search
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Detection of Hits not perfect #75

Open JordanVV opened 2 years ago

JordanVV commented 2 years ago

Hi,

I have some questions regarding the results I obtained. I was looking for a gene cluster conserved in roughly all the genomes I have included into my local databases (135 genomes, cerated from genbank files, codes works, no error popped up).

1st issue : When I open either the output or the clinker results, several genes within this gene cluster are not detected in several genomes while they share 99 id over 98 coverage (check manually)...

Issue 1

2nd issue: WE miss a lot of genomes in the analysis, 59 are screened over the 115 that the local database contains.

issue2

We tried to change many parameters already: filtering by -me -mi -mc, changed the level of sensitivity -ds... always missing genes inside clusters and missing clusters in a lot of genomes from our local database.

Thank you for your help

JV

gamcil commented 2 years ago

Hi @JordanVV, sorry for not getting onto this. Thanks to @brymerr921 this should hopefully be fixed with https://github.com/gamcil/cblaster/pull/77, now in cblaster v1.3.13. Could you see if you still have the same problem?