Regarding use of reference genome for SQANTI3

ConesaLab / SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes

GNU General Public License v3.0

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Closed Upendra19993 closed 8 months ago

Upendra19993 commented 8 months ago

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 8 months ago

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.