Question: Primary assembly or patches: what to choose for making index file?
0
gravatar for piyushjo
18 months ago by
piyushjo170
piyushjo170 wrote:

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!

index hisat2 genome • 511 views
ADD COMMENTlink written 18 months ago by piyushjo170

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

ADD REPLYlink written 18 months ago by h.mon28k

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

ADD REPLYlink written 18 months ago by piyushjo170
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