Showing posts from July, 2015

Genome methylation analysis with Bismark

Bismark is currently the de facto standard for primary analysis of high throughput bisulfite sequencing data. Bismark can align the reads to the genome and perform methylation calling. In this post, I'll go through Illumina whole genome bisulfite sequence (WGBS) alignment and methylation calling using Bismark. First I want to mention that this post is just a summary, not meant to be a user manual or thorough troubleshooting guide. Fortunately, Bismark has some of the best documentation for any bioinformatics suite and is mandatory reading. The Bismark crew are very proactive with responding to user queries on various forums as well.

First step in getting Bismark to work is to index the genome, in this case with Bowtie2:

bismark_genome_preparation --bowtie2 /pathto/refgenome/

Conventionally, multiplexed libraries will be sequenced over a number of lanes. Resist concatenating or merging the smaller fastq files for each patient/sample until after the alignment, as the concatenated fil…

Weighing the benefits of RNA-seq error correction

Sequencing data contains two major types of errors, ones that are incorporated during library preparation and ones incorporated during sequence reading. While errors of the former are difficult to correct as they occur without clues from the base quality scores, the latter type do correlate with lower base quality scores and so it is possible to identify these ambiguous base calls and compare them to a library of high confidence k-mers from the same sequencing run. Error correction of this type has been show to improve de novo assemblies and SNP detection.

A recent report posted in bioRxiv shows error correction gives a drastic improvement in transcriptome assembly, with the author benchmarking the performance of five different correction software packages (Bless, Lighter, SGA, SEECER & BFC). The author reports that these software options vary in the aggressiveness of error correction, with SGA being the most aggressive, Lighter the least aggressive and BFC and SEECER performing w…