User: chloe.steen

gravatar for chloe.steen
chloe.steen120
Reputation:
120
Status:
Trusted
Location:
Oslo
Last seen:
7 hours ago
Joined:
1 year, 7 months ago
Email:
c******@ifi.uio.no

Posts by chloe.steen

<prev • 22 results • page 2 of 3 • next >
0
votes
3
answers
759
views
3
answers
Answer: A: Cancer CNV workflow
... First of all, Copy number Variation (CNV) are copy number variations present in normal cells. The ones you see in cancer cells are called Copy Number Aberrations (CNA). SNP6.0 array is probably the best platform to detect copy number aberrations. ASCAT is a very good software to detect copy number ...
written 15 months ago by chloe.steen120
1
vote
2
answers
786
views
2
answers
Answer: A: hg18 vs hg19 in SNP6.0 data
... I contacted Affymetrix directly, and they recommend to always use the latest version of the annotation file for the appropriate array. So for my case, that is the annotation file for GenomeWideSNP_6 Annotations, CSV format, Release 35 (313 MB, 4/30/15) (current latest release). The Annotation file ...
written 16 months ago by chloe.steen120
1
vote
2
answers
1.3k
views
2
answers
Answer: A: Sciclone on exome sequencing data
... New question: Does sciClone calculate/take into account tumor percentage when calculating VAF? Is there a way to give it as input? The reason I ask if because my VAF plots are not scaled to tumor percentage, and it looks as though the VAF of a subclone increases between primary and relapse, but ...
written 17 months ago by chloe.steen120
0
votes
2
answers
649
views
2
answers
Answer: A: SciClone not numeric error
... You can try the following: 1. Make sure your variant allele frequency variable is a value between 0 and 100. 2. Convert the vaf variable into a numeric variable, and/or convert your file into a dataframe For example for sample 1: v1 <- data.frame(v1) v1$vaf <- as.numeric(v1$vaf) ...
written 17 months ago by chloe.steen120
2
votes
1
answer
456
views
1
answers
Answer: A: Measuring tumor heterogeneity
... I am not sure what kind of data you have, and I may have misunderstood your question, but here are anyway some tools that look at tumor heterogeneity, the clonality of the tumor and tumor purity, as well as evolutionary progression between several samples from the same patient. This list is probably ...
written 17 months ago by chloe.steen120
0
votes
2
answers
786
views
2
answers
Comment: C: hg18 vs hg19 in SNP6.0 data
... Thank you for your answer. I am not sure if I can use liftover with Genome-wide Human SNP6.0 array data, I don't have sequencing data. Do you have experience with using liftover on SNP6.0 data? ...
written 17 months ago by chloe.steen120
2
votes
2
answers
786
views
2
answers
hg18 vs hg19 in SNP6.0 data
... I have SNP6.0 data that were generated in 2010-2011. I use ASCAT to process them, and on the ASCAT website it is recommended to use PennCNV to create the LogR and BAF-files. In [ASCAT's protocol][1], they suggest using hg19 as build in the PennCNV procedure. I was wondering if anyone knows how usi ...
hg19 ascat hg18 penncnv snp6.0 written 17 months ago by chloe.steen120
0
votes
2
answers
1.3k
views
2
answers
Comment: C: Sciclone on exome sequencing data
... I thought I would just include as a final comment in my post where I read about using ASCAT for WES in the Sciclone paper: > As with other tools [6], [11], [22], [30], regions of CNA and LOH are > provided as inputs after having been inferred from whole-exome > sequencing (WES, e.g., via A ...
written 18 months ago by chloe.steen120
0
votes
0
answers
606
views
0
answers
Comment: C: ASCAT input files
... Just for clarification so that I maybe can answer your question, what is your goal? To prepare the LogR and BAF-files so that you can run ASCAT to get copy number profiles of your sample? Or have you already run ASCAT? ...
written 18 months ago by chloe.steen120
0
votes
2
answers
1.3k
views
2
answers
Comment: C: Sciclone on exome sequencing data
... Thanks Chris for the very quick response! I will try as you said, and hopefully it will work after I go through my variant calls, and use another tool for copy number prediction. ...
written 18 months ago by chloe.steen120

Latest awards to chloe.steen

Popular Question 5 months ago, created a question with more than 1,000 views. For Sciclone on exome sequencing data
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Only one cluster in multiple tumor phylogeny samples

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 952 users visited in the last hour