bisulfite methylation alignment rate

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2.9 years ago

francesca3 ▴ 150

Hi everyone, I'm starting to analyze some some bisulfite methylation data from mouse cortexes. I'm noticing that the alignation rate is between 35 and 40 %. I read that also other people experienced this problem. I tried both with bsmap and bismark but the result it is the same.. It is a common and an expected issue? I don't have really exeprience in this field and with rna-seq data the ratio is at least double. I have PE data with around 300 millions reads for fastq. Thanks Francesca

bisulfite methylation bsmap alignment bismark • 1.2k views

ADD COMMENT • link updated 2.9 years ago by Devon Ryan 104k • written 2.9 years ago by francesca3 ▴ 150

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That's super low, I typically get 90%+ for well characterized genomes. What organism is this? Did you try the non-directional option with bismark? I suspect that's the issue.

ADD REPLY • link 2.9 years ago by Devon Ryan 104k

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yes, my sequences are not directional and I put that option both in bismark and bsmap. Did you ever try to use this tool to estimate the bisulfite conversion ratio? https://github.com/hqyone/BCR_Evaluator. Apparently it seems that the my ratio is very low according to this tool. Thanks

ADD REPLY • link 2.9 years ago by francesca3 ▴ 150

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I've not used that tool, I just calculate it from the MethylDackel output. The conversion rate won't affect the alignment rate.

ADD REPLY • link 2.9 years ago by Devon Ryan 104k

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