Page Comparison

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Aim:

This page provides tips on how to cluster oligonucleotide sequences (i.e., aptamers, miRNAs, etc) based on the their sequence identity using two strategies: 1) mapper.pl script from the mirdeep2 package, and 2) cd-hit clustering approach.

Pre-requisites

• Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html )

• Basic unix command line knowledge (example: https://researchcomputing.princeton.edu/education/external-online-resources/linux ; https://swcarpentry.github.io/shell-novice/ )

• Familiarity with one unix text editors (example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

Method 1: Clustering oligonucleotide sequences (i.e., aptamers, miRNAs or small RNAs)

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mapper.pl S32_19to21nt.rename.fasta -c -m -s S32_19to21nt.collapsed.fa

Where:

-c input is a fasta file (see above for other input options)

-m merge identical sequences and generate its copy number

-s output filename

Example: Merged identical sequences showing copy number (i.e., _x57828)

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