Entering edit mode
19 months ago
m90 ▴ 30
I downloaded in my terminal indexed file of UCSC hg19 and when I uncompressed it, I found two files
genome.8.ht2. Every time I want to align my samples at indexed file this error show up
[e::bwa_idx_load_from_disk] fail to locate the index files command exited with non-zero status 1
So, my question is: Which one of two files I should use and how use
file.ht2 in alignment?
it didnt work still have the same problem because uncompressed folder has two files that i dont know which one of them i should assign in my path
(ERR): "/home/ngs/workdir/hg19" does not exist Exiting now ...
You can try /home/ngs/workdir/hg19/genome. Also, when you use a software, read it document is a good idea, just use command 'hisat -h', and it will solve most of your confusion.
<ht2-idx> Index filename prefix (minus trailing .X.ht2).
This is wha I downloaded before when I used hisat2 in sequence alignment.