Annotating DMR/DMS

[harish0201]

Hi!

I've started using the toolkit and have found some DMRs and DMSs. As per the faq, you have mentioned I can intersect the outcomes using bedtools to annotate the genes.

Do I need to merge the DMR windows or DMS over a window and then annotate with the bed file?

Any suggestion is appreciated!

[guoweilong]

I guess you need. The regions predicted by cgmaptools dmr might be very close. You may want to extend them to some distances and try to see if they can be merged as a large one.

While, if you are looking for the bedtools intersect region, and then unique these regions/merged these regions for counting, it may be a similar way.

Best,
Weilong

[harish0201]

Alright, will try that and get back to you. Thanks for the software! It runs very fast!

[hmyh1202]

cool

Another question for DMS and DMR analysis：
how to do DMS or DMR using more than two sample: such as sam1 and sam2 versus sam3 and sam4.

[guoweilong]

You can try to merge two CGmap files into one.
Following commands may help:
cgmaptools merge2 cgmap # for merging two CGmap files to one CGmap file
cgmaptools mergelist tosingle # for merging multiple CGmap files into one CGmap file.

Best,
Weilong