Chip-seq

[archana bhardwaj]

Hello 

I am new to this tool . Trying to get the figure as per paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064796/figure/F4/ A and B. 

I have chip seq data. I predicted chip peak using macs (for each peak calling used control and input file). Right now I am using Density array method. 

1) i have uploaded peak region (or it could be TSS region based on our desired prediction ..right ??? )

2) under step 2 , load aligned reads , should i upload control and input file both ?? How it will extract the data from two bam files and plot heatmap and profile ?? 

Or should i use Enrichment method  because it has option to add control file (must be looking  for the control bam files as used under peak calling) 

I am bit confused . Please help me to figure it out. 

Another question is i have RNAseq data. Third option under seqminer is Advance(RNA-seq). How can i use it for my RNAseq data interpretation ?? 

waiting for reply 

[archana bhardwaj]

wiating for reply :(