Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Methylation, statistics and methylated regions

    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,

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-27-2024, 06:37 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X