How to properly use and understand chip-seq analysis with DiffBind ?
0
0
Entering edit mode
@pierremarin-17659
Last seen 3.9 years ago

Hi everybody !

I'm a PhD student trying to analyse Chip-seq data generated in my project but I'm loosing it to use properly DiffBind package even if I read several times the manual.

To illustrate my work :

Chip-seq on flies:

  • 3 Lineages (A, B and C) x 3 treatments control included (CT, PQ, CO) x 2 histones mark K4 and K9 x 2 replicas per conditions (ov1 and ov2)

= 36 samples analyzed, 18 for K4 and 18 for K9.

My questions are :

  1. Effect of treatments per lineage ?:

          In lineage A i want to contrast control (CT) against CO or PQ and the same thing for other lineages

  1. Effect of lineages per treatment? :

         In treatment CO, difference between A and B , B and C...

If I understand the Diffbind package usage :

  1. I imported data in a csv format with .bam file for sequence informations, and peak caller data obtained from Peak ranger software               
ID TISSUE FACTOR CONDITION REPLICATE INTERVALS
A_CT_k4_ov1 A K4 CT 1  
A_CT_k4_ov2 A K4 CT 2  
A_CO_k4_ov1 A K4 CT 1  
A_CO_k4_ov2 A K4 CT 2  

 

I used to import :

samples_k4 <- read.table(data-sheet) 
chip_k4 <- dba(sampleSheet =samples_k4)

Then I used the count option which count peaks in the peak caller datasif I understand but I didn't understand if it use information of input data given

chip_k4_count <- dba.count(chip_k4, summits = 250, bParallel = F)

After counting I used the option to generate contrast

chip_k4_contrast <- dba.contrast(chip_k4_count,  categories = c(DBA_CONDITION, DBA_TISSUE)

To show contrast possibility I used

dba.show(chip_k4_contrast, bcontrast = T)

And now problems...

For example the contrast between lineages, group1 = A vs group2 = B take all sample of the lineage A and B so control and other treatment together...

But I want group1 = A:CT vs group2= B:CT How to use a fixed factor as the treatment, I tried with block option without success.

How work Diffbind with replicas ? Because I want to made Ven Graph after and when i tried, I obtained graph with specific replicas and no a global effect.

  Thanks for every effort to help me !

diffbind chip-seq R • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 625 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6