User: garrisrg

gravatar for garrisrg
garrisrg10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
5 years ago
Joined:
5 years, 1 month ago
Email:
g*******@gmail.com

Posts by garrisrg

<prev • 7 results • page 1 of 1 • next >
0
votes
3
answers
1.3k
views
3
answers
Answer: A: Good way to get location of in-del SNPs in UCSC coordinates?
... Thanks Martin that did the trick, I'll be sure I have the source file from now on. Here's the comparison with both genomes: NCBI: > library('BSgenome.Hsapiens.NCBI.GRCh38') > genome<-BSgenome.Hsapiens.NCBI.GRCh38 > start3<-rep(42126499,10) > #CYP2D6 seq strings for NCBI build ...
written 5.0 years ago by garrisrg10
0
votes
3
answers
1.3k
views
3
answers
Answer: A: Good way to get location of in-del SNPs in UCSC coordinates?
... Hi again Martin, I tried to reproduce the sequence issue I was talking about. Curiously the problem seemed to show up with the BSgenome.Hsapiens.UCSC.hg19_1.3.99, although I've never really seen it for this one before: > library("BSgenome.Hsapiens.UCSC.hg19") > genome2<-BSgenome.Hsapiens ...
written 5.0 years ago by garrisrg10
0
votes
3
answers
1.3k
views
3
answers
Comment: C: Good way to get location of in-del SNPs in UCSC coordinates?
... Thank you Martin I will give the developer version a try. I figured there might be a way with the new GRCh38 packages but I was somewhat hesitant as I attempted to retrieve a few sequences from  BSgenome.Hsapiens.NCBI.GRCh38 and found myself having similar problems as in this post: https://stat.ethz ...
written 5.0 years ago by garrisrg10
1
vote
3
answers
1.3k
views
3
answers
Good way to get location of in-del SNPs in UCSC coordinates?
... Hi guys, My question is somewhat related to this one posted almost 2 years ago: https://support.bioconductor.org/p/50306/. I am curious if there is any quick way to retrieve in-del snps that give USCS coordinates like the SNPlocs.Hsapiens.dbSNP.20120608 package? I know I can retrieve them using the ...
snp snplocs written 5.0 years ago by garrisrg10
0
votes
4
answers
2.2k
views
4
answers
Answer: A: 'external_gene_id' error when invoking the BiomartGeneRegionTrack function
... Hi Florian, Thanks for your quick answer. I've been using R for sometime but am somewhat new to bioconductor so I was a little unsure where to get up-to-date information concerning package issues. I figured there was no way I could have been the only person with this problem, but a number of google ...
written 5.1 years ago by garrisrg10
0
votes
4
answers
2.2k
views
4
answers
Answer: A: 'external_gene_id' error when invoking the BiomartGeneRegionTrack function
... Seems the issue with the BioMartGeneRegion was resolved in the latest patch for Gviz: 1.10.1. Not sure when this patch was released or why it didn't update on my computer properly, but it seems after re-installing the VariantAnnotation package as well as Gviz it works beautifully. Thanks again! ...
written 5.1 years ago by garrisrg10
0
votes
4
answers
2.2k
views
4
answers
'external_gene_id' error when invoking the BiomartGeneRegionTrack function
... Hi, I"m looking to visualize the relative locations of SNPs in a particular gene region and I've been able to get all track functions to work except the BiomartGeneRegionTrack. Since I have downloaded the SNP information from "hsapiens_snp" dataset I'd like to use a GeneRegionTrack that will give m ...
biomart gviz written 5.1 years ago by garrisrg10 • updated 5.1 years ago by florian.hahne@novartis.com1.6k

Latest awards to garrisrg

Popular Question 5.0 years ago, created a question with more than 1,000 views. For Good way to get location of in-del SNPs in UCSC coordinates?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For 'external_gene_id' error when invoking the BiomartGeneRegionTrack function

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 378 users visited in the last hour