Sequence Alignment/Map (SAM) format is a well-known bioinformatics format designed to store information about reads mapping against large reference sequence. The SAM file is split into two sections: a header section and an alignment section. The header section starts with ‘@’ and it contains information such as the name and length of the reference sequence. […]
Read MoreAll technologies, have their advantages and disadvantages, and next generation sequencing (NGS) is no different. For the time being, the current dominant forces in NGS are Illumina, which is based upon detecting a flash of light as fluorescent nucleotides are incorporated, or Ion Torrent, where nucleotide incorporation is detected in the form of a change […]
Read MoreIn the different RNA-Seq experiments, we have found that some experiments have more significant DE (differential expression) genes than others. Besides the experiment design which is the most important factor, a number of other factors may influence the number of DE genes. Here, we list the different experiments that we have carried out the investigation […]
Read MoreAll bioinformatics server users and administrators would know how easy it is to fill up our home directories with huge amounts of data, especially when you are analysing deep sequencing data on a daily basis. Here is a list of a few useful commands and tips that can help to keep your home directory tidy. […]
Read MoreWe recently managed to set-up an account on amazon web service (AWS) that will enable us to test out how practical and efficient it will be to do computationally intensive analyses in the cloud. We often wonder whether it is worth spending loads of money on new servers and lots of time managing the hardware […]
Read MoreThe first Viral Bioinformatics and Genomics training course held at the University of Glasgow was completed successfully by 14 delegates (nine external and five internal) on 10-14 August 2015. The course took place in the McCall Building computer cluster, and the adjacent Lomond and Dumgoyne Rooms were used for refreshments and lunch. Instructors: Joseph Hughes […]
Read MoreWe have recently written a review article entitled “Bioinformatics tools to analyse viral genomics data” for the OIE. In the review, we were unable to provide direct hyperlinks and references to all available tools, simply because there are too many, so we included them here. These commonly used bioinformatics tools are split into the following categories: […]
Read MoreHere are my slides from the BBSRC WestBio DTP skills training session at University of Glasgow, Friday 26th June 2015. The talk was entitled “Case studies of HTS applications” and presents a number of case studies on the application on high-throughput sequencing (HTS), also known as next generation sequencing (NGS), to biological problems ranging from human […]
Read MoreA few days back I posted a question on BioStars about getting genome accession numbers for a list of protein GIs. I had a long list of protein GI and I wanted the genome accession number for each protein GI (if there is one in NCBI databases) but without downloading files for each protein GI […]
Read MoreHere are the slides of my talk in Saskatoon if anybody is interested. The Saskatchewan, like the Glaswegians, are friendly but sometimes hard to understand. They certainly have trouble understanding me.
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