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Hi,
I'm posting after a look on the forum, and as a newbie, I admit that I didn't find the information I was looking for.
I'm now with already trimmed, aligned, sorted, bam file of WGBS (whole genome bi sulfite).
My mission is to get out of it statistics about that file as a preliminary job.
I looked on different softwares that could help me with, I found MethylExtract. I now also have VCF differenciating SNP and 5mC (but interestingly, I don't think I have non-methylated Cytosines).
My goal is to be able to characterize CpG Islands (where/how many), characterize CpG, telling if some regions are more methylated than others..
I think I have a good start with that VCF out of MethylExtract, but so far I can only see it on IGV.
* Is there a different software I can use to help me in characterizing all that, or should I do it with a script?
* Is my VCF sufficient at all ?
* What are the software post-bismark (used later in your pipeline than bismark) that you would use for that purpose?
* How can I have an estimation of Methylated CpG and non Methylated CpG (taken in account that some regions are hard to sequence, that doesn't correlate with the fact they are devoted or not of methylation)
* is there a way to annotate (like we could do with whole-exome sequencing) with genes?
Last question, one of my file is a woman (no Y sequences aligned), but I'm surprised to see that on that chromosome I can't find > 50% of Cytosines methylated in my bam file (seen on IGV) or a eye-judged higher methylation rate in that chromosome. Is that normal?
Thank you for all your answers,
I'm posting after a look on the forum, and as a newbie, I admit that I didn't find the information I was looking for.
I'm now with already trimmed, aligned, sorted, bam file of WGBS (whole genome bi sulfite).
My mission is to get out of it statistics about that file as a preliminary job.
I looked on different softwares that could help me with, I found MethylExtract. I now also have VCF differenciating SNP and 5mC (but interestingly, I don't think I have non-methylated Cytosines).
My goal is to be able to characterize CpG Islands (where/how many), characterize CpG, telling if some regions are more methylated than others..
I think I have a good start with that VCF out of MethylExtract, but so far I can only see it on IGV.
* Is there a different software I can use to help me in characterizing all that, or should I do it with a script?
* Is my VCF sufficient at all ?
* What are the software post-bismark (used later in your pipeline than bismark) that you would use for that purpose?
* How can I have an estimation of Methylated CpG and non Methylated CpG (taken in account that some regions are hard to sequence, that doesn't correlate with the fact they are devoted or not of methylation)
* is there a way to annotate (like we could do with whole-exome sequencing) with genes?
Last question, one of my file is a woman (no Y sequences aligned), but I'm surprised to see that on that chromosome I can't find > 50% of Cytosines methylated in my bam file (seen on IGV) or a eye-judged higher methylation rate in that chromosome. Is that normal?
Thank you for all your answers,