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miRDeep2 for small RNA sequencing

Hello,

I am using the following tutorial for microRNA profiling: https://drmirdeep.github.io/mirdeep2_tutorial.html

I was able to follow it until the patching step which is: bash patchme.sh

However the next step where we install the miRBase reference file gives an error as follows:

mirdeep2_patch abhaykanodia$ mirbase.pl 21
-bash: mirbase.pl: command not found

Can someone please let me know how to fix it? Thanks a lot!

microrna mirdeep2
• 3,861 views • link
written by abhay.kanodia • abhay.kanodia

If you see the miRDeep2 usage instructions on the screen you can continue to install the patch. Otherwise something went wrong during the installation.

Try the step before: perl install pl ??

• 0 views • link
written by M.O.L.S • M.O.L.S

Hi @M.O.L.S,

Thanks for your response. The problem is not with the patch argument which runs successfully and I can see the usage instructions. The problem is with the next command where mirbase.pl where it is not recognized and says "command not found."

(base) MacBook-Pro-3:mirdeep2 abhaykanodia$ cd /Users/abhaykanodia/mirdeep2_patch
(base) MacBook-Pro-3:mirdeep2_patch abhaykanodia$ bash patchme.sh
File /Users/abhaykanodia/mirdeep2/bin/miRDeep2.pl has been moved to /Users/abhaykanodia/mirdeep2/bin/miRDeep2.pl.orig and the current /Users/abhaykanodia/mirdeep2_patch/miRDeep2_patch.pl has been linked to /Users/abhaykanodia/mirdeep2/bin/miRDeep2.pl
(base) MacBook-Pro-3:mirdeep2_patch abhaykanodia$ mirbase.pl 21
-bash: mirbase.pl: command not found
• 0 views • link
updated by Ram Ram • written by abhay.kanodia • abhay.kanodia

Another point: Unless the directory containing mirbase.pl is in your PATH, you should run it using the absolute/relative path to the script. If it's the current dir, ./mirbase.pl might work where mirbase.pl fails.

• 0 views • link
written by Ram Ram

1 answer

Perhaps you could type the word perl before mirbase.pl in order to run the program. If it is already installed it should run the same as other perl programs. This might work.

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updated by Ram Ram • written by M.O.L.S • M.O.L.S

Great! Thanks a lot. Will try that. I have added my code if that helps.

• 0 views • link
written by abhay.kanodia • abhay.kanodia

Adding perl before mirbase.pl actually worked. Thanks so much. Wow!

• 0 views • link
written by abhay.kanodia • abhay.kanodia

That's great abhay ! glad you got it working you can accept the answer , and continue your bioinformatic analysis.

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written by M.O.L.S • M.O.L.S

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