Our lab is doing more and more WGBS libraries (human) - and we sporadically sequence a weird library that aligns poorly (~15% vs usual ~80% with bismark2) and has a weird base composition profile - however if we repeat the library prep from scratch it works fine.
Here's the fastqc plot.
Has anyone seen this? It appears our bisulfite conversion isn't being very efficient. We are using the Illumina protocol - except we use a homebrew bisulfite method instead of the epitect kit - we've never had problems with our homebrew method for other applications ie PCR based methylation sequencing.
Any suggestions/ideas?
Here's the fastqc plot.
Has anyone seen this? It appears our bisulfite conversion isn't being very efficient. We are using the Illumina protocol - except we use a homebrew bisulfite method instead of the epitect kit - we've never had problems with our homebrew method for other applications ie PCR based methylation sequencing.
Any suggestions/ideas?
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