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How can I confirm that I installed bcl2fastq correctly?

Hello,

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?

Thank you

bcl2fastq linux ubuntu
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written by bioinfo • bioinfo

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 bcl2fastq long term.

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written by GenoMax GenoMax

I am using bcl2fastq very often but we are changing servers so I need to set up everything again.

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written by bioinfo • bioinfo

1 answer

shouldn't it be

export PATH=/data/Resources/bcl2fastq2-v2-20-0-linux-x86-64/usr/local/bin:$PATH

? (not /bcl2fastq after bin)

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you. That worked.

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written by bioinfo • bioinfo

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