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Prepare Reference Files
The reference files required for making the MappingConfig file is listed below
I download reference FASTA from the UCSC genome browser. For mapping, I will keep all the small contigs to make sure all reads mapped properly, but I usually remove them and only focus on the main chromosomes for further analysis.
For human and mouse, we usually use GENCODE's latest version. But I do not update GTF throughout the same project. (And the difference between versions probably have little impact on your analysis results.)