align using file.ht2

1

now i downloaded in my terminal indexed file of UCSC hg19 and when i uncompress it , i found two files genome.5.ht2 genome.8.ht2 and 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 ?


ht2


indexing


bioinformatics


hisat2

• 23 views

updated 1 hour ago by

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written 2 hours ago by

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20

You should put the index in a separate folder and when you use hisat2 you should enter the index folder not the index file, just like this: hisat2 -p 10 -x dir/genome -1 fq -2 fq

1 hour ago by


ry

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