User: C Lin

gravatar for C Lin
C Lin60
Reputation:
60
Status:
Trusted
Location:
United States
Last seen:
3 days, 20 hours ago
Joined:
5 years, 3 months ago
Email:
b*****@hotmail.com

Posts by C Lin

<prev • 28 results • page 1 of 3 • next >
0
votes
1
answers
1.5k
views
1
answers
Comment: 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 4 days ago by C Lin60
0
votes
1
answers
1.5k
views
1
answers
Comment: C: DESeq2 PCA plot on fitted values
... *moved it down ...
written 4 days ago by C Lin60
0
votes
2
answers
391
views
2
answers
Comment: 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 9 months ago by C Lin60
0
votes
2
answers
391
views
2
answers
Comment: 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 9 months ago by C Lin60
6
votes
2
answers
391
views
2
answers
reads alignment statistics
... 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, ...
rsubread bioconductor written 9 months ago by C Lin60 • updated 9 months ago by Hervé Pagès ♦♦ 13k
0
votes
1
answer
352
views
1
answer
PCR bottleneck coefficient (PBC)
... 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? ...
chipqc written 11 months ago by C Lin60 • updated 11 months ago by Rory Stark2.5k
0
votes
1
answers
1.3k
views
1
answers
Comment: C: Technical details of DiffBind correlation analysis
... Can you please explain what is the score in the occupancy analysis? is it the peak's height? peak's intensity?   ...
written 11 months ago by C Lin60
0
votes
0
answers
315
views
0
answers
Comment: C: ChIPQC plotCoverageHist() and plotCC() not showing inputs
... Hi, I am also trying to make the input and ChIP curves plot on the same graph. Did you figure this out?  ...
written 11 months ago by C Lin60
0
votes
1
answers
214
views
1
answers
Comment: 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 12 months ago by C Lin60
0
votes
1
answer
214
views
1
answer
ChIPQC plots for input samples
... 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 ...
chipqc written 12 months ago by C Lin60 • updated 12 months ago by Thomas Carroll390

Latest awards to C Lin

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 132 users visited in the last hour