'Bowtie2 error : " does not exist or is not a Bowtie 2 index"
I'm very new to bioinformatics and RNA-seq so go easy on me. I keep getting the same error when I try perform my analysis. For background: I have a folder called tutorial, in the folder there are 4 other folders (important ones for now are trimmed_fastq, bt2Index and insert_size). Using bowtie2-build, I created a the bt2 files with the index Zv9 in the bt2Index folder. Now I want to align my trimmed reads (in trimmed_fastq) to the genome.
here's what I do and the error I get:
cd desktop/tutorial/insert_size
bowtie2 \
--minins 0 \
--maxins 1000 \
--very-fast \
-x $HOME/desktop/tutorial/bt2Index/Zv9 \
-1 $HOME/desktop/tutorial/trimmed_fastq/2cell1.trim.paired.fq \
-2 $HOME/desktop/tutorial/trimmed_fastq/2cell2.trim.paired.fq \
-S 2cells.sam
(ERR): "/Users/eag519/desktop/tutorial/bt2Index/Zv9" does not exist or is not a
Bowtie 2 index
Exiting now ...
I've tried writing it out in several different ways but can't solve it. Any ideas? Any help would be much appreciated. I'm a complete beginner.
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