Computational biology and genomics
I will be giving a workshop titled “Reproducible Bioinformatics” at BioC Asia tomorrow. I have been thinking a lot about this topic and my aim for the workshop is to introduce computational tools and demonstrate how they can be used to help promote reproducibility when performing bioinformatic analyses. Ensuring reproducibility shouldn’t be an extra burden…
I’m a big fan of the book Bioinformatics Data Skills by Vince Buffalo and I highly recommend it to everyone who works in the bioinformatics field. The book introduces the reader to The Golden Rule of Bioinformatics, which is: Never ever trust your tools (or data). I am a strong proponent of this rule, which…
A quick guide to organizing computational biology projects has been published over 8 years ago but the main messages are still very relevant (perhaps even more so nowadays given the exponential increase in biological data). In a nutshell, computational biology projects need to be organised so that we can share and reproduce our work in…
Updated 2018 March 23rd for R-3.4.4 I use a lot of shortcuts provided by GNU Readline. I recently compiled R without Readline support and it was almost unusable! This was because I ran into the error: configure: error: –with-readline=yes (default) and headers/libs are not available To circumvent this I compiled R by running: ./configure –with-readline=no…
Update: 2015 August 19th: I discovered the “Retrieve Metadata from PDF” feature in Zotero that can retrieve all the metadata from a PDF and adds all the relevant information. (This doesn’t work for all PDFs but for the majority it works. Note that if you perform too many queries, Google Scholar will restrict you from…
Updated 2014 September 19th to include a method that does not require sorting. The h-index is an index that is calculated by measuring the number of articles, say $$n$$, that has at least $$n$$ citations. If you published 10 articles, and each of them had four citations, your h-index would be four, since there are…
2014 August 11th: I noticed that some people are coming across this post by googling “bioinformatics data skills pdf”. IMHO, this book is well worth the 40 dollars (price of the ebook) and I’m sure the author went through a lot of hard work to get it published, so please compensate him for his work….
I’ve tried to explain the BAM flags to my colleagues and I think each time I have left them more confused. So perhaps I can do a better job of explaining BAM flags in writing. For this post, I will use this BAM file from the 1000 Genomes Project: NA18553.chrom11.ILLUMINA.bwa.CHB.low_coverage.20120522.bam.
Updated: 2014 May 14th; added even more tips I’m in the middle of writing papers and my thesis, so I’ve been quite busy. However, I wanted to write a quick blog post as an outlet. So here’s a list of random command line tips off the top of my head (GNU bash, version 4.1.2(1)-release); I…
I asked a question on Twitter about sorting a really huge file (more specifically sorting a huge BED file). To put really huge into context, the file I’m processing has 3,947,386,561 lines of genomic coordinates. I want the file to be sorted by the chromosome (lexical order), then by the start coordinate (numeric order) and…