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Old 11-22-2013, 06:24 AM   #1
feralBiologist
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Default Combination of paired-end and single-end samples in Chip-seq TF study

I have 2 batches of chip-seq samples:

(A) One biological SE replicate

This batch, actually, consists of 4 SE Chip-seq samples - one treatment, one control, both have IP controls. All are SE sequenced at a lab A

(B) Two biological PE replicates

This batch consists of 8 PE Chip-Seq samples - 2 treatment, 2 controls, all have IP controls. All are PE sequenced at a lab B.

The idea is to establish differential binding between the treatment and the controls. I plan to use macs and diffbind but I am open to suggestions.

My first specific question is how to treat the PE samples. I see 3 options:

(1) Treat all forward and reverse reads as SE reads

(2) Take just the forward or the reverse reads

(3) Treat each PE sample as, essentially, 2 technical replicates (one consisting of forward reads, one of reverse)

I find (3) intuitively attractive but, again, I am open to suggestions. If I go for it than the model would need to introduce 2 additional factors - one accounting for the technical replicates, another for the batch effect. So far I have dealt with batch effects only - I presume that adding additional factor shall be straight-forward but, please, let me know if there are things that I need to pay attention to.

Last edited by feralBiologist; 11-23-2013 at 11:51 AM.
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