User: asif.zubair

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Posts by asif.zubair

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Comment: C: csaw: removing PCR duplicates using dedup flag
... Sure. I think I might have missed this, but thank you for pointing it out. So, csaw relies on bams in which duplicates have already been marked. ...
written 3.2 years ago by asif.zubair0
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csaw: removing PCR duplicates using dedup flag
... Hi,  csaw allows one to remove PCR duplicates when doing read counting across windows. My question is how is this functionality actually executed. I generally mark duplicates using Picard Tools or Samblaster and I was of the view that csaw would remove these reads when doing read counting. However ...
csaw dedup written 3.2 years ago by asif.zubair0 • updated 3.2 years ago by James W. MacDonald52k
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Comment: C: dumpPE in csaw on multiple bam files.
... Thank you, Aaron. This helps!  ...
written 3.6 years ago by asif.zubair0
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csaw: post clustering description of regions
... For csaw's merge operation over windows, my understanding is that the merge operation simply clusters nearby windows into a region. It doesn't pay heed to the direction of the FC or if the windows have significant DB. Is this understanding correct ?  However, an obvious issue then is how do we defi ...
csaw mergewindows written 3.6 years ago by asif.zubair0 • updated 3.6 years ago by Aaron Lun25k
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csaw: when not to dedup
... In the csaw workflow and vignette, it is mentioned that duplicate removal is not always advisable. I couldn't quite understand why that would be. Shouldn't duplicate removal help prevent false positives ?  ...
csaw dedup written 3.6 years ago by asif.zubair0 • updated 3.6 years ago by Aaron Lun25k
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csaw: dumpPE on multiple bam files.
... The new version of csaw introduced the very helpful dumpPE function to improve efficiency of downstream methods.  However, is one expected to use this method one file at a time or can multiple files be supplied.  For example, csaw suggests this: outBam <- dumpPE(bamFile, "whee", param=xparam, ...
csaw dumppe windowcounts written 4.0 years ago by asif.zubair0
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Comment: C: Issue with RUVs
... Yes, I think you are right.  By sensible I meant that the replicates don't cluster together as I would like. However, simply by using the DESeq size factors, it works.  I like RUVSeq approach and so wanted to try it on my dataset as well. Particularly interesting was the counter intuitive argument ...
written 5.2 years ago by asif.zubair0
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Comment: C: Issue with RUVs
... Hi Davide, Thank you, it worked ! Can I use my normalized counts directly for an analysis by say edgeR ?  Best,  Asif  ...
written 5.2 years ago by asif.zubair0
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Answer: A: Issue with RUVs
... I plotted the PCA for my normalized counts but it doesn't give anything sensible. I did normalization using DESeq's size factor estimation algorithm and it gives me sensible results. The function call I made is below: ruv_de = RUVs(data.matrix(de), genes, k=1, differences) x=rep(c(1,2,3,4,5,6),2) ...
written 5.2 years ago by asif.zubair0
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Issue with RUVs
... Hi,  I am trying to use RUVs to normalise my data. I have 12 samples which are replicated in pairs.  i.e. I can specify my differences like this: differences = matrix(data= seq(1,12,by=1), byrow=TRUE, nrow=6) where each row is a biological replicate I create a "counts" matrix which is n X 12 m ...
ruvseq ruvs eda written 5.2 years ago by asif.zubair0

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