Hi Ramya,
I have two questions.
First, can we bypass/change the coverage threshold to pass QC?
One of my data set seems to have a lot more trans interaction. I just want to go ahead with the analyses to see what can be interpreted from it.
wt_samples has < than 40% ( 22.8468056561234 %) reads in cis. Does not pass QC.
wt_samples has < than 40% ( 14.3283582089552 %) coverage near the bait. Does not pass QC.
patients has < than 40% ( 30.0322089252988 %) reads in cis. Does not pass QC.
patients has < than 40% ( 19.7014925373134 %) coverage near the bait. Does not pass QC.
Second, can we have different number of replicates for different conditions?
for example:
samples = c("wt1","wt2","wt3","pat1","pat2","pat3","pat4","pat5")
conditions = c("WT","patient")
replicates = c(3,5)
Hi Ramya, I have two questions. First, can we bypass/change the coverage threshold to pass QC? One of my data set seems to have a lot more trans interaction. I just want to go ahead with the analyses to see what can be interpreted from it.
wt_samples has < than 40% ( 22.8468056561234 %) reads in cis. Does not pass QC. wt_samples has < than 40% ( 14.3283582089552 %) coverage near the bait. Does not pass QC. patients has < than 40% ( 30.0322089252988 %) reads in cis. Does not pass QC. patients has < than 40% ( 19.7014925373134 %) coverage near the bait. Does not pass QC.
Second, can we have different number of replicates for different conditions? for example: samples = c("wt1","wt2","wt3","pat1","pat2","pat3","pat4","pat5") conditions = c("WT","patient") replicates = c(3,5)
Thanks a lot