Hisat2 alignment error

Question

[Ashish]

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 ...

Answer 1

[ATpoint]

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.