Hisat2 alignment error

Hi, I have prepared index by providing splice junction and exon information genome_trans but I'm getting an error during mapping

"index file does not exist"

Command line

(base) macserver@MACs-Mac-Pro hisat2_alingment % hisat2 -p 8 -x /Users/macserver/Desktop/buffalo_refence_genome/buf_rna_index -1 /Volumes/AshishIVRI/OLD/ashishanalysis/Trim_F/Gr_11_R1C.fastq -2 /Volumes/AshishIVRI/OLD/ashishanalysis/Trim_F/Gr_11_R2C.fastq -s /Users/macserver/Desktop/hisat2_alingment/Gr_11.sam
(ERR): "/Users/macserver/Desktop/buffalo_refence_genome/buf_rna_index" does not exist Exiting now ...

hisat2

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updated 3.6 years ago by Ram

• written 3.6 years ago by Ashish •

1 answer

The -x must be the basename of the index, so if you have files like (I think they're named like that) idx.1.ht2, idx.2.ht2 (...) then it is simply -x path/to/idx. It is not the enclosing folder but the basename of the actual index files.

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written 3.6 years ago by ATpoint