Aim:
This page provides tips on how to cluster oligonucleotide sequences (i.e., aptamers, miRNAs, etc) based on their sequence identity using two strategies: 1) mapper.pl script from the mirdeep2 package, and 2) cd-hit clustering approach.
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Once installed you will be able to access the mapper.pl script. This script will be used to merge merges sequences that are 100% identical sequences and generate their also generates the copy count for each unique sequence (i.e., seq1_x578 ; seq1 has 578 copies). The available parameters options are:
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| Code Block |
|---|
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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