Uncategorized Archives - CVR Bioinformatics

4th Annual Training Course on Viral Bioinformatics and Genomics (20-24th Aug, 2018)

September 12, 2018
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From 20-24th Aug, we have held our 4th Viral Bioinformatics and Genomics training course at the Garscube campus of the University of Glasgow. In this year, our course had 16 participants attending from academic and health institutions from across the UK, Europe, Canada, Australia, Qatar, and South Africa. The MRC-University of Glasgow Centre for Virus […]

July 17, 2018
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What is weeSAM? weeSAM is a python script which produces coverage statistics and coverage plots from an input SAM or BAM file. Figures and stats are written up in HTML so users can easily view the coverage for their reference assembly. weeSAM is simple to run and the steps below give an illustration. What’s new […]

October 23, 2017
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For the 3rd year running, we have held our Viral Bioinformatics and Genomics training course at the Garscube campus of the University of Glasgow. The course took place from Monday 7th August – Friday 11th August 2017, with 16 participants attending from academic and health institutions from across the UK, Europe, USA, Uganda, and Saudi […]

July 19, 2017
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FAST5 format from Oxford Nanopore (ONT) is in fact HDF5, which is a very flexible data model, library, and file format for storing and managing data. It is able to store an unlimited variety of datatypes. A number of tools have been developed for handling HDF5 available from here. The most useful are: hdfview, a […]

August 10, 2016
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We have shared our knowledge on Viral bioinformatics and genomics with yet another clever and friendly bunch of researchers. Sixteen delegates from across the world joined us for a week of intensive training. The line-up of instructors changed slightly due to the departure of Gavin Wilkie earlier in the year. Instructors: Joseph Hughes (Course Organiser) […]

April 20, 2016
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Here are my slides from a session on NGS data formats and analyses that I gave as part of the EPIZONE Workshop on Next Generation Sequencing applications and Bioinformatics in Brussels in April 2016. It covers file formats such as FASTA, FASTQ, SAM, BAM, and VCF, and also goes over IUAPAC nucleotide ambiguity codes, read names, quality […]

November 19, 2015
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November 16, 2015
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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. […]

November 9, 2015
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All 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 […]

November 2, 2015
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In 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 […]

Archives

4th Annual Training Course on Viral Bioinformatics and Genomics (20-24th Aug, 2018)

weeSAM version 1.5.

3rd Viral Bioinformatics and Genomics Training Course (7th – 11th August 2017)

Exploring the FAST5 format

2nd Viral Bioinformatics and Genomics Training Course (1st – 5th August 2016)

NGS Data Formats and Analyses

Simple Bash Quiz

Java CIGAR Parser for SAM format

The dark arts of Ion Torrent Sequencing

Some key factors for number of significant DE genes

Training Courses