Methylkit with BS-Seeker 2

[david....@gmail.com]

Hi Everybody,

I am quite new to DNA methylation analysis, and I have a question regarding usage of methylkit. People in my group have used BS-Seeker 2 to align BS-seq data on Arabidopsis genome. I wanted to know if it is possible to use these files with methylkit (and if yes, how can I load them)? I tried to follow methylkit tutorial, but could not manage to load my files. If it is impossible, does anyone have a suggestion on which tool I should used to find differentially methylated regions or compare methylomes?

Sincerely

David

[Altuna Akalin]

If BSseeker provides CpG location, percent/ratio of methylation and coverage information as a text file you can use it. Otherwise, I recommend Bismark 

Best,

Altuna

--
You received this message because you are subscribed to the Google Groups "methylkit_discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to methylkit_discus...@googlegroups.com.
To post to this group, send email to methylkit_...@googlegroups.com.
Visit this group at https://groups.google.com/group/methylkit_discussion.
For more options, visit https://groups.google.com/d/optout.

[david....@gmail.com]

Hello Altuna,

Thank you for your very swift answer. My lab has a pipeline that post-process the aligned sam files into a text file with information for each cytosine like this one:

CHR    POS    STR    CONTEXT_1    CONTEXT_2    BASES_METH    BASES_STR    BASES_TOT    METH_LEVEL
1         298      F        CAA                 Z                      0                         1                     1                      0.000
1         310      F        CGA                X                      1                         1                     1                      1.000
1         311      R        CGT                X                      0                         0                     1                      NA

Where Chr = Chromosome, Pos = genomic position, STR = strand, Context = methylation context (CHG, CPG, CHH), Bases_meth = number of reads with the methylated cytosine, bases_str = number of read with unmethylated cytosine, base_tot = total number of reads mapping at this position (including other strand reads) meth_level = % of reads with methylated cytosine at this position.

Would it be enough to use methylkit? In which way should I edit this file to load it in methylkit?

Again, thank you very much for your time and help.

Sincerely

David

[Altuna Akalin]

see this post: http://zvfak.blogspot.de/2012/10/how-to-read-bsmap-methylation-ratio.html

You may need to filter that file before using to be able to use in methylKit. I think strand column should also be - or +.

You have to make it look like a generic file with minimal information, chr,start,strand,methylation ratio/percentage, coverage. See the post above.

Best,

Altuna

--

[guowe...@gmail.com]

Hi David and everybody,

Thanks for using BS-Seeker2. As BS-Seeker2 output standard format such as CGmap and ATCGmap formats.

Recently, we have developed novel software pipeline, named CGmapTools (https://cgmaptools.github.io ), which comprise of 39 functions with processing CGmap or ATCGmap formats, can be used for DNA methylation anlaysis, coverage analysis, CNV analysis, ASM analysis.

Hope you find it useful!

Best,

Weilong Guo