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Could not locate a HISAT2 index to basename

Hello everyone I am first time trying to use HISAT, I am getting the following error message

I am using the following command: /usr/bin/hisat2 -p 10 --dta -x usr/bin/rn6/genome -1 Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R1_001.fastq.gz -2 Documents/Shaima/Seq/Pros/S/WS020_S6_L002_R2_001.fastq.gz -S WS020_h.sam
It gave me the following error message: Could not locate a HISAT2 index corresponding to basename "usr/bin/rn6/genome"

Any help Thanks

rna-seq
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updated by Biostar Biostar • written by saj98 saj98

1 answer

You are likely missing a leading / in path for index name usr/bin/rn6/genome in your command. You need to provide qualified relative or full paths for files in your command.

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written by GenoMax GenoMax

Yes, I corrected the path, now is running

Thank you

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written by saj98 saj98

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