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error in hisat2 alignment

Hi

I would like to align fastq , I use below command:

./hisat2  -q  --add-chrname  -x  /home/baydaa70/hisat_indexes/h19/genome   /home/baydaa70/Desktop/trimmed.fastq -S /home/baydaa70/Desktop/out.sam

but I got an error:

Could not locate hisat2 index corresponding to basename /home/desktop/index files/h19/genome

Please help me

Thanks in advance.

hisat2
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updated by Ram Ram • written by molashahimaryam • molashahimaryam

Can you show us output of ls -lh /home/baydaa70/hisat_indexes/h19/?

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written by GenoMax GenoMax

could not locate hisat2 index corresponding to basename /home/desktop/index files/h19/genome Thanks

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written by molashahimaryam • molashahimaryam

You already posted the error in your original post. In order to address that I was asking that you run the command in my comment and show us the output. We need to see what files you have in that directory. If you don't want to post the output (if there are other files there) at least show us what you see with ls -lh /home/baydaa70/hisat_indexes/h19/genome*.

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written by GenoMax GenoMax

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