Assessing genetic variants

One of the projects I have been involved with is SeqNextGen, where I'm analysing exomes of patients who have a suspected rare genetic disorder. It's a change from what I was previously researching during my PhD; instead of working on an RNA level, I've reverse transcribed1 and I'm now examining DNA sequence and analysing genetic...

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Getting started with analysing DNA sequencing data

I have recently entered new territory and started working on analysing DNA sequencing data (as opposed to analysing RNA sequencing, i.e. transcriptomics). While it is still the analysis of lots of sequencing reads, one of the goals is to identify disease causing mutations; this is in contrast to identifying differentially expressed genes or inferring gene...

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Getting started with paired-end reads

I've wanted to write this post for a while, but I never had to work with paired-end libraries, so the impetus wasn't quite there. Finally I've decided to take a look at some paired-end libraries at work and as usual, I will test some simple examples before I touch the real data. For those not...

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How deep should we sequence?

Updated 2013 November 12th. High throughput sequencers are continually increasing their output of reads; according to Illumina, the HiSeq2500/1500 can output a maximum of 187 million single end reads per lane/flow cell. The question is "How deep should we sequence our samples?" Obviously it depends on the aim; if we wish to profile lowly expressed...

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