User: dirigible2012

gravatar for dirigible2012
dirigible2012310
Reputation:
310
Status:
Trusted
Location:
European Union
Last seen:
2 years, 7 months ago
Joined:
3 years, 12 months ago
Email:
d************@gmail.com

about me

Posts by dirigible2012

<prev • 27 results • page 1 of 3 • next >
0
votes
0
answers
749
views
0
answers
Ancestry Inference with known Founder Genotypes
... I have a yeast population bred by intercrossing the descendants of four founder strains. We have SNP data for the descendants, and the founders are fully sequenced. I would like to discover QTL in this population. To account for the effects of population structure, at every SNP I need to find the p ...
qtl ancestry hmm snp yeast written 2.7 years ago by dirigible2012310 • updated 2.7 years ago by Biostar ♦♦ 20
0
votes
0
answers
826
views
0
answers
GWAS with more than two alleles per locus
... I am trying to find the genes responsible for trait variation in a yeast population. The population was produced by several generations of interbreeding starting with the F2 descendants of a cross between four inbred lines. Strain A and Strain B were bred to produce Population 1 (F1 generation). St ...
qtl gwas population structure multiallelic written 2.7 years ago by dirigible2012310
0
votes
0
answers
991
views
0
answers
LOD Intervals with Multiple QTL Mapping in r-qtl
... Hello all, I am trying to use r-QTL with the new Multiple QTL Mapping functions. I know how to run the analysis and get the LOD profile, but I don't know how to analyse the results. I would like to get either a Bayes interval or a 1.5 LOD support interval, but the book I am using (A Guide to QTL Ma ...
qtl R r-qtl mqm written 2.8 years ago by dirigible2012310
3
votes
1
answer
1.1k
views
1
answer
Slow Download From TCGA
... Is anybody else having problems with a slow download of files from TCGA? At the moment it's taking me 1 hour to download 1 Gb of data using the File Search. My downloads of files from other sources run at about 5MB/second. Is there anything I can do about this? Thanks, Stephanie ...
tcga written 3.0 years ago by dirigible2012310
0
votes
0
answers
942
views
0
answers
Broad Firehose mRNA z-scores
... Hello all, I am still trying to find a place where I can download z-scores for the TCGA RNAseq data. I have found two mentions of z-scores being calculated automatically and available in Broad Firehose: https://confluence.broadinstitute.org/display/GDAC/mail/62337976 https://confluence.broadinst ...
firehose z-score rna-seq written 3.0 years ago by dirigible2012310
7
votes
1
answer
2.7k
views
1
answer
Per Cancer Bulk Download from CBioPortal
... I would like to download the mRNA expression z-scores for all genes (in all patients, with all cancers) from CBioPortal. I've found the download page, but I have to enter a list of genes I want the z-scores for - I don't want particular genes, I want to download all of them. This data is normally a ...
cbioportal cancer written 3.0 years ago by dirigible2012310 • updated 3.0 years ago by B. Arman Aksoy1.2k
5
votes
1
answer
1.6k
views
1
answer
CNV and Clinical Data for Cancer - Alternative to TCGA or ICGC
... Hello all, Last time I asked about cancer datasets on here somebody very kindly directed me to the TCGA, which was perfect! I'm now trying to confirm my results with another dataset. Does anybody know of any cancer datasets which include both CNV and clinical data? (I don't need very complicated cl ...
icgc tcga cnv cancer written 3.0 years ago by dirigible2012310 • updated 3.0 years ago by Obi Griffith16k
5
votes
1
answer
1.7k
views
1
answer
TCGA CNV/SNP6 Reference Sequence - hg19
... Hello all, The Broad Institute did the CNV analysis for the TCGA samples. The only information I have been able to find about the reference genome* does not give the version of hg19 they are using. I have two questions: 1. Is hg19 exactly the same as Ensembl's GRCh37?  2. It looks from the Ensemb ...
tcga reference genome snp cnv hg19 written 3.2 years ago by dirigible2012310 • updated 3.1 years ago by Sean Davis23k
0
votes
2
answers
1.5k
views
2
answers
Answer: A: TCGA Barcodes Missing from Bulk Data
... Found the answer - The Bulk Download appears to be mainly for downloading historic versions of the archives, and doesn't seem to provide file to barcode mapping. The File Search tool is the answer for downloading the LATEST version of the archive. Each download will contain a "file_manifest.txt" f ...
written 3.2 years ago by dirigible2012310
10
votes
3
answers
6.7k
views
3
answers
TCGA/Broad Institute CNV Files Segment Mean
... Hello everybody, I am trying to analyse CNV data from TCGA to get a measure of overall CNV per patient. When I download the Level 3 files taken from the SNP6 array, there is a column in the file called Segment_Mean. (Example at bottom.) What do the numbers in this column represent? I think they ...
tcga cnv written 3.2 years ago by dirigible2012310 • updated 5 months ago by kingsire0

Latest awards to dirigible2012

Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Survival Analysis Using Tcga Data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 890 users visited in the last hour