Primary assembly or patches: what to choose for making index file?

Question

[piyushjo]

Hi,

I am restating my question which I earlier posted with incorrect details. I am confused between choosing the primary assembly file hg38.fa or the newer patches for making my index file using hisat2-build option.

And also if I make an index file without using annotation file (.gtf), would it still be a good index file? I am unable to make an index file using .gtf file with hisat2-build option because my computers run out of memory.

Thanks!

[h.mon]

Why don't you download the index provided by the hisat2 team:

ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38_snp_tran.tar.gz

[piyushjo]

I have done that for usual purpose, but I am trying to make one for lncRNA using gencode or lncipedia annotation file.