This post should show you an easy way to get the following data type integrated into a figure:
functional enrichment analysis gene expression data from any technology miRNA expression data from any technology I am using the function isoNetwork from the package isomiRs, that of course is developed by me :) My ego is not that big, it is just I wanted a figure showing that information, and I couldn’t find any at a time, but if you know any, tweet me about it to @lopantano.
MicroRNAs (miRNAs) are small RNA molecules (20-27 nt long) that are involved in eukaryotic gene regulation. They regulate targeted genes by RNA complementarity, generally between the miRNA seed region and the 3’ UTR of messenger RNAs. They have …
In summary: I will show which is the best miRNA mapping tool. I used several options for this benchmarking:
miraligner from SeqBuster suit (I am one of the authors) bowtie2 and bowtie novoalign from novocraft suit GEM srnabench microrazer STAR miRExpress I think that these are the most used, and other not used but good to try them. They were clearly developed for other purposes, but as well, they generate the input of many miRNA pipelines.
My PhD was focused on small RNA sequencing data. I had a problem when I wanted to visualized the amount of small RNAs from the beginning. Here the problem, assume that you have a certain distribution of small RNA sequences abundance:
seq1: 1500 times
seq2: 3 times
seq3: 2 times
And you want to show the nucleotide composition of the first nucleotide. You can do it either counting the # of sequences (or abundance) in your set (1505) or the number of unique (different) sequences (3).