I am trying to learn Bowtie and I couldn't figure out the error.
First, I downloaded GRCH38 build from NCBI assembly (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.39) and using the command bowtie2-build, built indexes of the reference sequence. Got four index bt2 files Then downloaded fasta sequence from NCBI SRA (http://ftp.sra.ebi.ac.uk/vol1/run/ERR235/ERR2356727/24_1.fastq.gz) (http://ftp.sra.ebi.ac.uk/vol1/run/ERR235/ERR2356727/24_2.fastq.gz)
Then aligned with reference sequence using the command: bowtie2 -x GCF_000001405.26_GRCh38_genomic.fna.fna -U 24_1.fastq,24_2.fastq -S eg1.sam
I get the following error: "GCF_000001405.26_GRCh38_genomic.fna.fna" does not exist or is not a Bowtie 2 index
I used the bowtie2 commands to align the sequence but still getting an error. Can someone help with the error here? Is there a way to make sure that I have Bowtie 2 index files