User: nadne

gravatar for nadne
nadne40
Reputation:
40
Status:
New User
Location:
European Union
Last seen:
2 years, 7 months ago
Joined:
5 years, 5 months ago
Email:
n****@walla.com

Posts by nadne

<prev • 11 results • page 1 of 2 • next >
0
votes
5
answers
16k
views
5
answers
Comment: C: Converting Illumina Raw Genotype Data Into Plink Ped Format
... You can find the module [here][1] and it's super easy to export to plink format. [1]: http://support.illumina.com/downloads/genomestudio-plug-ins.html ...
written 3.1 years ago by nadne40
0
votes
2
answers
3.0k
views
2
answers
Answer: A: Why Are These Snps On The Wrong Strand Compared To The Reference Genome
... Check out [this resource][1] for updating strands, and A/B mapping. [1]: http://www.well.ox.ac.uk/~wrayner/strand/ ...
written 3.4 years ago by nadne40
0
votes
2
answers
3.0k
views
2
answers
Answer: A: Why Are These Snps On The Wrong Strand Compared To The Reference Genome
... Did anyone resolved that? ...
written 3.4 years ago by nadne40
2
votes
2
answers
2.0k
views
2
answers
Answer: A: Recalling SNPs count from Illumina SNP array raw data
... I finally ended up using R package named crlmm. It has a function named genotype.Illumina that does the recalling given the raw idat files. ...
written 3.6 years ago by nadne40
0
votes
2
answers
2.0k
views
2
answers
Comment: C: Recalling SNPs count from Illumina SNP array raw data
... That's probably true, and yet, I want to see what was the genotyping in the raw calls, before imputation was done. In addition, it is not obvious how to use IMPUTE2 with these files. ...
written 3.7 years ago by nadne40
0
votes
2
answers
2.0k
views
2
answers
Comment: C: Recalling SNPs count from Illumina SNP array raw data
... I have the PLINK, but I want to process the raw data, as the bim-bed-fam files have manny missing calls, and I'm trying to figure out why, or can I recall it. I tried using CRLMM, and it reads the idat files, and gives two number for each SNP: calls and confidence. But do I do with this two? How do ...
written 3.7 years ago by nadne40
4
votes
2
answers
2.0k
views
2
answers
Recalling SNPs count from Illumina SNP array raw data
... I want to recall SNPs from Illumina HumanOmni2.5-4v1. I have the raw data (Grn.idat and Red.idat) files, and also a matching FinalReport.csv which include the next columns: SNP Name Sample Name GC Score Allele1- Forward Allele2- Forward Allele ...
illumina snp written 3.7 years ago by nadne40
0
votes
1
answer
4.4k
views
1
answers
Comment: C: From genotype raw data .idat to PLINK files
... I encounter the same error. Have you manage to solve that? ...
written 3.7 years ago by nadne40
0
votes
1
answer
3.2k
views
1
answers
Comment: C: Blastp -outfmt Problem With Format Specifiers
... Error could not be reproduced on my system. Is genomax2's comments works for you? ...
written 3.9 years ago by nadne40
0
votes
0
answers
1.3k
views
0
answers
Filtering phyloseq object by sample ids
... I have a phyloseq object and I would like to filter by sample ids read from a text file. How can I do that? ...
R phyloseq filtering microbiome written 3.9 years ago by nadne40

Latest awards to nadne

Scholar 3.6 years ago, created an answer that has been accepted. For A: Recalling SNPs count from Illumina SNP array raw data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2736 users visited in the last hour