HISAT2 - soft-masked genome from UCSC

Question

[lshepard]

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.

Answer 1

[Matt Shirley]

If you take a look at the HISAT2 source code (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);
    ...

[lshepard]

Thanks Matt! It would have been nice to have this clear on the manual, but I have actually just noticed that some of their pre-built indexes are from UCSC, so that is re-assuring.