I tried to install bcl2fastq2 Conversion Software v2.20 Installer (Linux rpm). I installed it using the directions from this link: https://kb.10xgenomics.com/hc/en-us/articles/360001618231-How-to-troubleshoot-installing-bcl2fastq- Installation created a user folder and I tried to set the path using: export PATH=/data/Resources/bcl2fastq2-v2-20-0-linux-x86-64/usr/local/bin/bcl2fastq:$PATH However, when I did bcl2fastq version it does not seem to be able to find it.
Does that mean that I did not install it correctly? I realized later that I should had installed it like this: yum install -y bcl2fastq2-v2-20-0-linux-x86-64.rpm but I thought that since it seemed like the files were unpacked that it was ok. Should I delete the usr file that was created the first time I installed it and try it again?
What exactly are you trying to do? If you are simply trying to demultiplex 10x data then your sequence provider should/can do this for you very easily. Especially if you have no need to use
I am using bcl2fastq very often but we are changing servers so I need to set up everything again.