Homolog.us - Frontier in Bioinformatics


Woodford's WEIF Dead, Oxford Nanopore IPO Doubtful

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Pacbio Releases HiFi Data on Drosophila, Rice and Those Pesky Little Creatures (aka Humans)

All Against All Fight Breaks Out among the Sequencing Businesses

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Debugging RNAseq - (iv) Effective Length and TPM

In previous two posts on RNAseq concepts (here and here), we explained the inner workings of programs like Kallisto and Salmon based on a simple example. We also created a small simulated set identical to the example, ran Kallisto on it and got results matching theory.

Debugging RNAseq - (iii) Expectation Maximization Hands on

Debugging RNAseq - (ii) Core Concept - Expectation Maximization

We recently started a series on debugging RNAseq analysis. At presest, the programs used for analysis are used as black boxes, and the results are taken on faith. This becomes a problem, when the known genes do not show up as expected. Does that mean the prior knowledge is wrong, or the samples are prepared incorrectly, or some parameters/assumptions in the analysis programs are incorrect? Moreover, who will debug the analysis - bioinformaticians reading all relevant biology papers, or biologists learning about the analysis step?

Debugging RNAseq Analysis - (i)

In my experience, there are large disconnects between the bioinformaticians and biologists regarding RNAseq data analysis. In the current mode of operations, biologists send their samples to core sequencing labs, core sequencing labs send the FASTQ sequence files to ‘expert bioinformaticians’ and then the bioinformaticians pass derived tables to the biologists. Biologists publish, get money and the process starts once again.

Counting Quotient Filter and SeqOthello

Prashant Pandey, Rob Patro and collaborators published a number of excellent papers on a new kind of “compound” hashing scheme. The original paper discussing the idea is available at “A General-Purpose Counting Filter: Making Every Bit Count”, but they published other papers linking their idea to bioinformatics. We wrote about Mantis last year in this blog.

RNAseq Questions - How to Load and Combine Salmon Data in R?

Over the last year, I have been meeting many biologists and training them on NGS RNAseq data analysis. Sometimes they even bring their own research data to the class and learn to analyze as well as see results.

RNAseq Questions - Loading Many Kallisto Count Files in R

This is a continuation of our discussion from yesterday’s post. For general context, over the last year, I have been meeting many biologists and training them on NGS RNAseq data analysis. Sometimes they even bring their own research data to the class and learn to analyze as well as see results.

RNAseq Questions - How to Combine Gene Annotations (gff/gtf) with Kallisto Counts?

This is a continuation of our discussion from yesterday’s post. For general context, over the last year, I have been meeting many biologists and training them on NGS RNAseq data analysis. Sometimes they even bring their own research data to the class and learn to analyze as well as see results.

RNAseq Questions - How to Load and Combine Kallisto Counts in R?

Over the last year, I have been meeting many biologists and training them on NGS RNAseq data analysis. Sometimes they even bring their own research data to the class and learn to analyze as well as see results.

Tryst between Marilyn Monroe and Albert Einstein

You may have heard part of this story, where Marilyn Monroe told Einstein - “Would it not be wonderful if we had a child with your brains and my beauty?” Einstein replied promptly: “Yes, but imagine a child with my beauty and your brains!”

A Minimalist R Cheatsheet for NGS Biology

While teaching R to biologists, a common complaint I hear is that “there are too many functions”. Therefore, I decided to take a minimalist approach and not teach students new functions unless those are absolutely necessary. Using existing functions for new tasks has two benefits - (i) it keeps the brain clutter-free from too many function names, (ii) it gives students more practice on the existing functions thus reinforcing their knowledge.

Thousand Dollar Server for NGS Biology

These days, many biologists are performing RNAseq and other NGS experiments. The immediate challenges after collecting the data are (i) where to store them, (ii) where to analyze them and (iii) how to give access to all lab members in an efficient and secure manner.

Git Tricks to be Dangerous

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Hybrid Metagenomic Assembler OPERA-MS

Readers working on metagenome assembly will enjoy a new paper by Denis Bertrand et al that came out in Nature Biotech. I have not gone through the algorithm yet, but would like to do, when the authors make a pdf copy available.

Please Join Our Expert Membership Section

Dear readers, over the years many of you requested more organized content and complete tutorials on bioinformatics. Three years back, we started posting them in our membership section. All content in the membership section had been free with registration.

Genome Assembly is a Nearly Solved Problem with Long Reads

Dan Graur's Excellent Book Sold Only One Copy so Far

Recently I requested Dan Graur’s book (“Molecular and Genome Evolution”) through interlibrary loan (ILL). Little did I realize that I took away the only copy available in the US university libraries. For proof, I attach this request slip hidden inside. My copy came from Reed College, which is not far from where I live, but look where else it went to. The request slip shows that someone from Harvard University borrowed the same copy through ILL. Given the distance between Harvard (east coast) and Reed College (west coast), I came to the conclusion that no other copy was available in any library in between.

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