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Comparison of alignment software for genome-wide bisulphite sequence data.

Chatterjee A, Stockwell PA, Rodger EJ, Morison IM - Nucleic Acids Res. (2012)

Bottom Line: We sequenced reduced representation human genomes on the Illumina platform and efficiently mapped and visualized the data with different pipelines and software packages.We examined three pipelines for aligning bisulphite converted sequencing reads and compared their performance.This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.

ABSTRACT
Recent advances in next generation sequencing (NGS) technology now provide the opportunity to rapidly interrogate the methylation status of the genome. However, there are challenges in handling and interpretation of the methylation sequence data because of its large volume and the consequences of bisulphite modification. We sequenced reduced representation human genomes on the Illumina platform and efficiently mapped and visualized the data with different pipelines and software packages. We examined three pipelines for aligning bisulphite converted sequencing reads and compared their performance. We also comment on pre-processing and quality control of Illumina data. This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists.

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SeqMonk display of differential methylation from different aligners. About 75 bp trimmed read data for 18 × 106 reads were aligned against the Human genome GRCh37 build by Bismark. v0.23, RMAPBS v2.05 and BSMAP v1.2 for which the methylation is displayed, respectively, from top to bottom below the gene, mRNA and CDS panes. Methylated CpG positions are shown in the red panes for each aligner, and unmethylated CpGs are in the blue panes. The display is of a randomly selected 2.55 Mbp region of chromosome 1. The black boxes indicate some regions of significant difference in methylation.
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gks150-F1: SeqMonk display of differential methylation from different aligners. About 75 bp trimmed read data for 18 × 106 reads were aligned against the Human genome GRCh37 build by Bismark. v0.23, RMAPBS v2.05 and BSMAP v1.2 for which the methylation is displayed, respectively, from top to bottom below the gene, mRNA and CDS panes. Methylated CpG positions are shown in the red panes for each aligner, and unmethylated CpGs are in the blue panes. The display is of a randomly selected 2.55 Mbp region of chromosome 1. The black boxes indicate some regions of significant difference in methylation.

Mentions: We have visualized and compared the methylation tracks for three aligners in SeqMonk. Regions showing extensively methylated and unmethylated CpGs are generally comparable between the aligners. However, closer examination of some regions revealed large differences between the outputs from the aligners. Figure 1 shows CpG methylation tracks produced by three different aligners in a 2.55 Mbp region of chromosome 1 (a section chosen at random), which documents this behaviour.Figure 1.


Comparison of alignment software for genome-wide bisulphite sequence data.

Chatterjee A, Stockwell PA, Rodger EJ, Morison IM - Nucleic Acids Res. (2012)

SeqMonk display of differential methylation from different aligners. About 75 bp trimmed read data for 18 × 106 reads were aligned against the Human genome GRCh37 build by Bismark. v0.23, RMAPBS v2.05 and BSMAP v1.2 for which the methylation is displayed, respectively, from top to bottom below the gene, mRNA and CDS panes. Methylated CpG positions are shown in the red panes for each aligner, and unmethylated CpGs are in the blue panes. The display is of a randomly selected 2.55 Mbp region of chromosome 1. The black boxes indicate some regions of significant difference in methylation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3378906&req=5

gks150-F1: SeqMonk display of differential methylation from different aligners. About 75 bp trimmed read data for 18 × 106 reads were aligned against the Human genome GRCh37 build by Bismark. v0.23, RMAPBS v2.05 and BSMAP v1.2 for which the methylation is displayed, respectively, from top to bottom below the gene, mRNA and CDS panes. Methylated CpG positions are shown in the red panes for each aligner, and unmethylated CpGs are in the blue panes. The display is of a randomly selected 2.55 Mbp region of chromosome 1. The black boxes indicate some regions of significant difference in methylation.
Mentions: We have visualized and compared the methylation tracks for three aligners in SeqMonk. Regions showing extensively methylated and unmethylated CpGs are generally comparable between the aligners. However, closer examination of some regions revealed large differences between the outputs from the aligners. Figure 1 shows CpG methylation tracks produced by three different aligners in a 2.55 Mbp region of chromosome 1 (a section chosen at random), which documents this behaviour.Figure 1.

Bottom Line: We sequenced reduced representation human genomes on the Illumina platform and efficiently mapped and visualized the data with different pipelines and software packages.We examined three pipelines for aligning bisulphite converted sequencing reads and compared their performance.This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.

ABSTRACT
Recent advances in next generation sequencing (NGS) technology now provide the opportunity to rapidly interrogate the methylation status of the genome. However, there are challenges in handling and interpretation of the methylation sequence data because of its large volume and the consequences of bisulphite modification. We sequenced reduced representation human genomes on the Illumina platform and efficiently mapped and visualized the data with different pipelines and software packages. We examined three pipelines for aligning bisulphite converted sequencing reads and compared their performance. We also comment on pre-processing and quality control of Illumina data. This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists.

Show MeSH