Hi, 

I recently started using genomes from UCSC, but it seems like they only have soft-masked and hard-masked. Obviously I do not want to use masking for aligning RNA-seq and just wanted to check whether HISAT2 treats the lower-case sequences like the upper case ones to allow mapping to the entire genome regardless of repetitive sequences.

I could not find this information in the documentation, sorry if I missed!

Thank you in advance.


If you take a look at the HISAT2 [source code](https://github.com/infphilo/hisat2/blob/master/ref_read.cpp#L148) (which nobody should expect you to do) it appears that all FASTA characters are converted to their uppercase representation when reading the reference file:

    # ref_read.cpp
	while(c != -1 && c != '>') {
		if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A';
		uint8_t cat = asc2dnacat[c];
    ->  int cc = toupper(c);
        ...
