User: markus.riester
markus.riester • 490
- Reputation:
- 490
- Status:
- Trusted
- Location:
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day ago
- Joined:
- 3 years, 7 months ago
- Email:
- m*************@gmail.com
Posts by markus.riester
<prev
• 64 results •
page 1 of 7 •
next >
0
votes
1
answer
91
views
1
answers
Comment:
C: PureCN prepare environment error
... Hm, this shouldn't be that difficult.
Did you run samtools faidx GRCh38.d1.vd1.fa? This should probably warn you when something is wrong with the Fasta. ...
written 1 day ago by
markus.riester • 490
0
votes
1
answer
91
views
1
answers
Comment:
C: PureCN prepare environment error
... Glad you figured it out. Bioconductor should be able to work with uncompressed Fasta files if they are sorted (the official genome build Fasta files are). See the underlying ?scanFa function. ...
written 4 days ago by
markus.riester • 490
0
votes
1
answer
91
views
1
answers
... Hi,
you sure hg38.fa is the correct path to the FASTA file?
> path[1]="hg38.fa": The system cannot find the file specified ...
written 6 days ago by
markus.riester • 490
0
votes
1
answer
58
views
1
answers
... There is no consensus regarding cutoffs and it's probably best to use as continuous covariate when possible.
https://www.ncbi.nlm.nih.gov/pubmed/30643254 ...
written 3 months ago by
markus.riester • 490
1
vote
1
answer
408
views
1
answers
... 4300 somatic calls would be a lot even for WES. Is it possible there is a tumor/normal misalignment?
Otherwise, running it quickly with Mutect 1 would be an easy way to debug. Mutect 1 reports all variants, even if found in PoN or matched normal, so it's easier to figure out the impact of those.
...
written 4 months ago by
markus.riester • 490
0
votes
1
answer
260
views
1
answers
... If you have at least a few processed-matched normals, you can try https://github.com/lima1/PureCN (disclaimer: our tool). ...
written 7 months ago by
markus.riester • 490
0
votes
1
answer
366
views
1
answers
... Others are way more qualified to answer here since I'm not a germline person, but with average 10X, you have to accept that you don't have the power to detect heterozygosity for all sites. So you have to find a way to deal with the uncertainty. I'm sure there are standard ways of doing that for your ...
written 8 months ago by
markus.riester • 490
0
votes
1
answer
366
views
1
answers
... It probably depends for what you need allelic imbalance and how sensitive your detection of allelic imbalance needs to be. Is this RNA or DNA-seq? If the latter, what's the coverage? ...
written 8 months ago by
markus.riester • 490
0
votes
1
answer
366
views
1
answers
... Are you sure that's not a [XY Problem][1]?
[1]: https://en.wikipedia.org/wiki/XY_problem ...
written 8 months ago by
markus.riester • 490
0
votes
1
answer
391
views
1
answers
... See what you mean, but I think what CY means with library size is simply total sequencing read coverage. But maybe I was interpolating too aggressively. ...
written 11 months ago by
markus.riester • 490
Latest awards to markus.riester
Good Answer
3.0 years ago,
created an answer that was upvoted at least 5 times.
For A: WES or WGS analysis of cancer samples with no matched germline
Appreciated
3.0 years ago,
created a post with more than 5 votes.
For A: WES or WGS analysis of cancer samples with no matched germline
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1465 users visited in the last hour