DNA mtethylation data analysis

yusufkhan · 03-05-2017, 11:46 AM

Hi,

I want some problem in loading data to visualisation tools.

I want to do annotations for methylcytosines (mCs) in three sequence contexts: CG, CHH, CHG of two foxtail millet cultivars (IC4 & IC41) specifying following regions in the genome such as Gene, 3prime_UTR, 5prime_UTR, exon CDS, Intron, TSS, Promoter (1.5kb upstream), upstream (1.5kb), TE and smRNA

I have summary data of plant samples of two cultivars in the following format.

9 618 618 100 1 0
9 626 626 100 1 0
9 638 638 100 1 0
9 642 642 100 1 0
9 662 662 100 1 0
9 672 672 100 1 0
9 689 689 66.6666666666667 2 1
9 700 700 50 2 2
9 720 720 100 4 0
9 726 726 100 4 0

Please let me know how to proceed for analysis and visualize

Thanks in advance

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Webinar on DNA-Seq data analysis- Case studies	Strandlife	Illumina/Solexa	1	02-20-2017 11:04 PM
DNA Methylation Data Analysis Workshop	ecSeq Bioinformatics	Epigenetics	3	11-03-2016 07:14 AM
Epigenetics Workshop - DNA Methylation Data Analysis	ecSeq Bioinformatics	Events / Conferences	2	10-26-2016 12:29 AM
Epigenetics Workshop - DNA Methylation Data Analysis	ecSeq Bioinformatics	Bioinformatics	1	07-28-2015 10:37 PM
Use bowtie2 to analysis DNA-reseq data	Lv Ray	Bioinformatics	4	07-01-2014 05:35 PM

03-05-2017, 11:46 AM	#1
yusufkhan Junior Member Location: Delhi Join Date: Nov 2010 Posts: 2	DNA mtethylation data analysis Hi, I want some problem in loading data to visualisation tools. I want to do annotations for methylcytosines (mCs) in three sequence contexts: CG, CHH, CHG of two foxtail millet cultivars (IC4 & IC41) specifying following regions in the genome such as Gene, 3prime_UTR, 5prime_UTR, exon CDS, Intron, TSS, Promoter (1.5kb upstream), upstream (1.5kb), TE and smRNA I have summary data of plant samples of two cultivars in the following format. 9 618 618 100 1 0 9 626 626 100 1 0 9 638 638 100 1 0 9 642 642 100 1 0 9 662 662 100 1 0 9 672 672 100 1 0 9 689 689 66.6666666666667 2 1 9 700 700 50 2 2 9 720 720 100 4 0 9 726 726 100 4 0 Please let me know how to proceed for analysis and visualize Thanks in advance