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Published 20 hours ago • verified publisher icon wyp1125

Question on missing homologous pairs in the .colinearity file

Open Mandyzg opened this issue 4 years ago • 2 comments

Hello,

I have a question regarding the default implementation of MCScanX, As the manual suggested, I first run blastp and obtained the .gff and .blast file that were used as input for MCScan. In the .blastp file, I have noticed gene pairs with alignment e-value as low as 1e-110. However, these matched gene pairs were not shown in the .colinearity file after I run MCScanX. I have read through the manual and the paper, but still couldn't find any explanation for that. Can anyone please clarify?

Thanks in advance, Mandy,

Mandyzg avatar Sep 01 '20 05:09 Mandyzg

Hi @Mandyzg did you work out a solution to this?

Surbhigrewal avatar Nov 27 '23 14:11 Surbhigrewal