Open Abieskawa opened 1 month ago
Hi, I am trying to apply GINGER to do structural annotate my genome data. Here are my questions:
I finished soft masking with my genome (it takes days), and found that the hard masking is recommended here https://github.com/i10labtitech/GINGER/issues/2#issuecomment-1774895140. But I found that most of people suggest soft mask instead of hard mask in the forums (https://www.biostars.org/p/417941/). Should I use hard masking, or actually, soft masking is feasible?
Another issues is that is ginger possible to integrate annotation of those genome without any rna-seq data?
In your paper, you mentioned that you use GINGER-based parameters to evaluate EVM, how did those parameters calculated?
If one combine multiple RNA-seq data and input GINGER, will it filter those of relatively low expression genes?
Hi, I am trying to apply GINGER to do structural annotate my genome data. Here are my questions:
I finished soft masking with my genome (it takes days), and found that the hard masking is recommended here https://github.com/i10labtitech/GINGER/issues/2#issuecomment-1774895140. But I found that most of people suggest soft mask instead of hard mask in the forums (https://www.biostars.org/p/417941/). Should I use hard masking, or actually, soft masking is feasible?
Another issues is that is ginger possible to integrate annotation of those genome without any rna-seq data?
In your paper, you mentioned that you use GINGER-based parameters to evaluate EVM, how did those parameters calculated?
If one combine multiple RNA-seq data and input GINGER, will it filter those of relatively low expression genes?