ConesaLab/SQANTI3

Regarding use of reference genome for SQANTI3

Upendra19993 opened this issue · 1 comments

Upendra19993 commented

Hi,

When using the reference genome for the SQANTI3 as an input, should we use the masked genome or the unmasked genome? And does it affect the result?

Many thanks,
Upendra.

carolinamonzo commented

Hi @Upendra19993 that's up to you and your biological question.
This is not a SQANTI issue, it depends on your research aims.

If you start your analysis from FASTQs, SQANTI3 will use minimap2 to map to the genome you give it.

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