User: linouhao

gravatar for linouhao
linouhao0
Reputation:
0
Status:
New User
Last seen:
12 hours ago
Joined:
2 years, 8 months ago
Email:
l*******@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by linouhao

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answer
1.7k
views
1
answers
Comment: C: CNVkit - how many normal samples do I need for the pooled normal reference?
... so how should we select the normal samples, is there any suggestions, I noticed that you mentioned the bam files size, so is there any concrete methods I also noticed thta you mentioned metrics These statistics help quantify how “noisy” a sample is and help to decide which samples to exclude from a ...
written 4 days ago by linouhao0
0
votes
0
answers
127
views
0
answers
Comment: C: CNV callers for WES data
... not a good choice, cnvkit can do this, but the result is not good ...
written 11 days ago by linouhao0
0
votes
1
answer
267
views
1
answers
Comment: C: Noisy CNV background in old FFPE sample
... so is there any qc criteria for cnvkit of detecting wes, wgs, tr sequence, for example depth? because we often talk about low quality, but there often saying no concrete value for these. for example, you said larger bins for low quality FFPE,but what the value ,wes target bin to be 2000 instead of 2 ...
written 11 days ago by linouhao0
0
votes
1
answer
341
views
1
answers
Answer: A: cnvkit filtering low depth bins
... the doc is very unclear, I am also puzzled ...
written 11 days ago by linouhao0
0
votes
0
answers
224
views
0
answers
Comment: C: How are the log2 values in CNVkit .cnr files calculated?
... the doc is very unclear, the fix command used the reference, which used the normal and tumor sample data, and cnr just uses the cnn file from tumor and the reference, it filter some region, but the calculation is very unclear ...
written 11 days ago by linouhao0
0
votes
2
answers
691
views
2
answers
Comment: C: Noisy germline CNV data using CNVKit
... if using pool reference, does the paired control sample no longer used for analysing. can you share your command? I ran my command like this, but I do not find any criteria to find the noisy sample firstly, I used the batch command to get all the control samples target.cnn and antitarget.cnn # com ...
written 11 days ago by linouhao0
0
votes
0
answers
89
views
0
answers
how should I filter call.cns results according to cn depth p_ttest probes weight
... 1 the cnvkit doc seems to be much later than the conda version, and there is not a good explatation of how to filter the final rersults depending on cn depth p_ttest probes weight 2 in the doc https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=10x#reference, it mentioned "CNVki ...
cnv written 16 days ago by linouhao0
0
votes
0
answers
64
views
0
answers
cnvkit suitable read depth , R version, reliable cutoff
... Dear all, I do as the recommend, conda install cnvkit, but I met several questions cnvkit.py version 0.9.7 1 it install R 4.0.2, which is not compatible with many r packages, can I specify R version , such as 3.6.3, what is more, it overrided the R I ever installed 2 is there a recommended sequ ...
cnvkit cnv written 22 days ago by linouhao0
0
votes
2
answers
5.1k
views
2
answers
Answer: A: Help with understanding CNVkit output
... @Eric Talevich when using cnvkit export vcf, a site has no CN, but when using export bed, it report the last column cn number is 1, so which one is right? another question is whether cnvkit.py batch take tumor purity into consideration? thanks a lot ...
written 9 months ago by linouhao0
0
votes
1
answer
468
views
1
answers
Answer: A: Can CVNkit call CNV correctly at HLA genes region?
... facets maybe a good choice, but I do not know how to annotate the segement results ...
written 15 months ago by linouhao0

Latest awards to linouhao

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 2.3.0
Traffic: 886 users visited in the last hour