RnBeads vs Bismark .cov genomic coordinates

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Adrian Stankiewicz

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Feb 6, 2019, 5:31:39 PM2/6/19
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Hello!

I am trying to perform hierarchical clustering on RRBS data. I have selected a subset of differentially methylated CpG sites based on results of RnBeads analysis. Next I tried to use the coordinates for these sites to extract raw methylation values from .cov files (generated by bismark_methylation_extractor (https://github.com/FelixKrueger/Bismark/blob/master/bismark_methylation_extractor) ). Sadly, these two sets of coordinates (Bismark .cov vs RnBeads sites differential methylation) dont seem to match - they seem to be shifted by 1. RnBeads data was generated based on the same .cov files.

As far as I know both RnBeads and Bismark use 1-based coordinate system, but I am likely missing something...

I will appreciate help...

Best
Adrian

Fabian

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Feb 8, 2019, 11:49:33 AM2/8/19
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Hi Adrian,
Are you using the BED files exported by RnBeads? If so, BED files have been standardized to are 0-based, half-open intervals.

Best,
Fabian
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