Category Archives: science

miRNA annotation tools comparison

In summary: I will show which is the best miRNA mapping tool. I used 4 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 … Continue reading

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RNA-seq correction at gEuvadis

I will comment one of the step that is done with RNA-seq data by researchers from gEuvadis project. They sequenced 1000 HapMap individuals, and did a lot of analyses trying to decipher the transcriptome variability among population. I think that … Continue reading

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small RNA abundance [miss-] viz

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 … Continue reading

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Lying factor in figures

What is the lying factor in figures? It is the ratio between the difference of two numbers and the difference of the visualization of those two numbers. For instance: You have two groups, each group is represented by 4 and … Continue reading

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miRNA annotation: complex scenarios

Everybody who is working with microRNA knows about miRBase, it was the first miRNA catalogue. Everybody is using it to annotate small RNA sequences as miRNA or not. And it is great, and very helpfully…but there are some cases that … Continue reading

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visualizing small RNA mapping complexity

I spent all my PhD working with small RNA sequences data. The main problem was, always those sequences that map in multiple locations, also denominated ambiguous sequences. From the very beginning, this made that pipelines remove this kind of sequences … Continue reading

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visualizing science is also cool @polychart

One of my interest in science is finding new ways to visualize Big Data. Scientist are used to work with static visualization, that of course, is wonderful in the majority of the case. But it wouldn’t be better dynamic visualization … Continue reading

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