bisulfite methylation alignment rate
0
0
Entering edit mode
3 months ago
francesca3 ▴ 70

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 • 267 views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

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
1
Entering edit mode

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

Login before adding your answer.

Traffic: 2555 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6