Originally posted by cmccabe
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Here are the steps:
Code:wget https://github.com/BenLangmead/bowtie2/archive/master.zip unzip master.zip cd /home/dnascopev/Desktop/master make
Code:echo 'export PATH=$PATH:/home/dnascopev/Desktop/bowtie2-2.6.0' >> ~/.bashrc
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the build indexs is running:
Are these normal?
Code:Warning: Encountered empty reference sequence Warning: Encountered reference sequence with only gaps Warning: Encountered reference sequence with only gaps Warning: Encountered empty reference sequence Warning: Encountered empty reference sequence Warning: Encountered reference sequence with only gaps Warning: Encountered empty reference sequence
Code:bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa /home/dnascopev/Desktop/hg19_fasta/my_hg19
Code:cat *.fa > hg19.fa
Thank you .
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bowtie2-build: command not found
I downloaded the bowtie 2-2.3.5.1 for mac using the link:https://sourceforge.net/projects/bowtie-bio/
It was a zipped file so I unzipped it.
I opened the unzipped folder on the terminal and then typed the command:
(base) linglabs-ipro:bowtie2-2.3.5.1-macos-x86_64 linglab$ bowtie2-build
-bash: bowtie2-build: command not found
(base) linglabs-ipro:bowtie2-2.3.5.1-macos-x86_64 linglab$
Please Help!
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@sahil: Please go through this UNIX basics tutorial, if you are unfamiliar with the command line.
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