User: C Lin
C Lin • 60
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- 60
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- United States
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- 3 months ago
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- 5 years, 6 months ago
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Posts by C Lin
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C: DESeq2 PCA plot on fitted values
... Sorry to revive this old thread. But, I just want to make sure.
So, if I do
plotMDS(log(t( t(assays(dds)[["mu"]]) / sizeFactors(dds) ) + 1)
I am using the fitted values that include the batch effect, correct? So, if samples are closer together in this MDS plot, it should represents how similar t ...
written 3 months ago by
C Lin • 60
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C: DESeq2 PCA plot on fitted values
... *moved it down
...
written 3 months ago by
C Lin • 60
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C: reads alignment statistics
... Thanks for your help. I figured it out.
I ran bowtie retaining only unique mapped reads. Therefore, my bam file does not contain multiple mapped reads. Duh!
James, thanks again for your help.
...
written 12 months ago by
C Lin • 60
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C: reads alignment statistics
... Thanks for the hints on countBam. However, I still cannot get the number of uniquely mapped reads.
I thought the following should return number of multiple mapped reads. However, it returns 0 when I know there are multiple mapped reads. bowtie2 shows ~14 millions reads
file='input.bam'
countBam(f ...
written 12 months ago by
C Lin • 60
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... Hello...
Is there an R package that can calculate alignment statistics from bam/sam files? By alignment statistics I mean number of reads, number of reads uniquely mapped, number of reads mapped to multiple locations.
I found rsubread package can count number of reads that can be mapped. However, ...
written 12 months ago by
C Lin • 60
• updated 12 months ago by
Hervé Pagès ♦♦ 13k
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... Is there a way to calculate the PBC1 and PBC2 following ENCODE standard https://www.encodeproject.org/data-standards/terms/#library?
I thought ChIPQC calculate these but I cannot find it?
...
written 14 months ago by
C Lin • 60
• updated 14 months ago by
Rory Stark • 2.5k
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... Can you please explain what is the score in the occupancy analysis? is it the peak's height? peak's intensity?
...
written 14 months ago by
C Lin • 60
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... Hi,
I am also trying to make the input and ChIP curves plot on the same graph. Did you figure this out?
...
written 14 months ago by
C Lin • 60
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C: ChIPQC plots for input samples
... Tom, thank you so much for your quick reply.
Faceting by tissue and color by factor gets me closer. However, it still do not plot the input. It's probably because I didn't specify the samples sheet correctly. So, in my samples sheet, I previously only listed my ChIP samples and in bamControls the p ...
written 15 months ago by
C Lin • 60
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... I have generated a QC report on my 35 samples (28 ChIP and 7 input samples) using:
ChIPQCreport(proj1.all,facet=F).
How do I generate plots with the corresponding input file on one graph?
For example: CCPlot seems to have all samples and only have 1 legend replicate.
My sample sheet and the plo ...
written 15 months ago by
C Lin • 60
• updated 15 months ago by
Thomas Carroll • 400
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