User: C Lin

gravatar for C Lin
C Lin60
Reputation:
60
Status:
New User
Location:
United States
Last seen:
2 months, 1 week ago
Joined:
4 years, 8 months ago
Email:
b*****@hotmail.com

Posts by C Lin

<prev • 26 results • page 1 of 3 • next >
0
votes
2
answers
278
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 10 weeks ago by C Lin60
0
votes
2
answers
278
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 10 weeks ago by C Lin60
6
votes
2
answers
278
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 10 weeks ago by C Lin60 • updated 8 weeks ago by Hervé Pagès ♦♦ 13k
0
votes
1
answer
151
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 4 months ago by C Lin60 • updated 4 months ago by Rory Stark2.1k
0
votes
1
answers
1.1k
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 4 months ago by C Lin60
0
votes
0
answers
229
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 4 months ago by C Lin60
0
votes
1
answers
137
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 4 months ago by C Lin60
0
votes
1
answer
137
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 4 months ago by C Lin60 • updated 4 months ago by Thomas Carroll390
0
votes
2
answers
132
views
2
answers
Answer: A: ChIPQC reading more samples that it should
... Thank you, Thomas for your reply. I figured out the issue. Turns out, some of the path to bamReads and bamControl have extra spaces causing the error above. ...
written 4 months ago by C Lin60
0
votes
2
answers
132
views
2
answers
ChIPQC reading more samples that it should
... Hi, I am trying to run ChIPQC. In my samples sheet I have 3 samples with the same input file and 2 samples with the same input file. So the total of files is 5 samples + 2 input. However, ChIPQC is "Computing metrics for 8 samples...". I am guessing this is why the error message is triggered at the ...
chipqc written 4 months ago by C Lin60

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: 379 users visited in the last hour