User: shiyang93

gravatar for shiyang93
shiyang9320
Reputation:
20
Status:
New User
Location:
Last seen:
4 weeks ago
Joined:
10 months, 3 weeks ago
Email:
s********@pku.edu.cn

Posts by shiyang93

<prev • 16 results • page 1 of 2 • next >
0
votes
0
answers
104
views
0
answers
Blacklist and greylist in PCAWG
... HI I want to do some analysis on the data from PCAWG(Pan Cancer Analysis of Whole Genomes), and I found some samples are labeled as Whitelist, some greylist and some blacklist. I guess that samples in greylist and blacklist are abnormal and not proper for downstream analysis, but I cannot find the o ...
icgc tcga pcawg written 29 days ago by shiyang9320
0
votes
2
answers
3.4k
views
2
answers
Comment: C: How to use MutSigCV correctly
... HI, Alien I have some difficulties in using MutSig. I am looking for solutions and find your answer here. I think you must be an expert in bioinformatics. Could you help me? I don't have the coverage file, so I use the full coverage file provided by MutSig. I also follow the guide by using 6 argumen ...
written 5 months ago by shiyang9320
0
votes
0
answers
203
views
0
answers
MutSig categ discovery failure
... HI I am using the mutsig to analyze my data. I not that mutsig has an preprocess step to calculate the categ column from the MAF input file. This step requires a genome reference file for its inference. However, though I include the genome build files in my input as below: MutSigCV('F:LUSC.MutSigCV ...
genome software error written 5 months ago by shiyang9320
0
votes
0
answers
210
views
0
answers
Comment: C: TCGA RNAseq files
... Oh, I got the data from cBioportal, sorry for providing incomplete information. It seems that cBioportal has done some analysis with the raw data from TCGA. the data can be acessed here: http://www.cbioportal.org/study?id=coadread_tcga#summary Thanks ...
written 5 months ago by shiyang9320
0
votes
0
answers
210
views
0
answers
TCGA RNAseq files
... Hi I am now working with the colorectal cancer project in TCGA, and want to analyze some gene expression data. I download the files, but do not know which is the gene expression file. I guess that it is the data_expression_median.txt file, but what is the meaning of median in this file? I cannot ass ...
rna-seq written 5 months ago by shiyang9320
0
votes
1
answer
281
views
1
answers
Comment: C: How to set the blast database of TopHat-Fusion
... Thank you very much! By the way, there are only human_genomic.00 -08, 10 - 16, 18 -21 on the blast database, no 09 and 17. I do not know if this human_genomic* database is intact. Could you give me some advice? ...
written 6 months ago by shiyang9320
0
votes
1
answer
281
views
1
answer
How to set the blast database of TopHat-Fusion
... I am using tophat fusion. My RNA-Seq data are from human, do I need to download the other_genomic* and nt* database from blast database as suggested by the user manual of TOPHAT-Fusion? http://ccb.jhu.edu/software/tophat/fusion_tutorial.shtml Anyone who is familiar with tophat can tell me? Thanks! ...
tophat gene fusion database blast written 6 months ago by shiyang9320 • updated 6 months ago by Istvan Albert ♦♦ 75k
0
votes
1
answer
266
views
1
answers
Comment: C: How to locate a locus on the genome and get the Exon/Intron No.
... But there are too many locus, need a lot lot lot of time to view them one by one. ...
written 7 months ago by shiyang9320
0
votes
1
answer
266
views
1
answer
How to locate a locus on the genome and get the Exon/Intron No.
... HI, I have a set of locus: chr2:123456-234567......,now I want to know if this locus is on a gene, if it is, then on which exon/intron? Because there are too many locus, viewing on the genomebrowser one by one is not practical. I also have tried softwares such as ANNOVAR, ONCOTATOR, but they only te ...
genome sequence snp written 7 months ago by shiyang9320 • updated 7 months ago by EagleEye4.9k
0
votes
0
answers
225
views
0
answers
Parameters for ABSOLUTE on WGS data
... I want to use ABSOLUTE to estimate the purity of my WGS data. I have called the SNCA by BIC-seq and feed the seg data to ABSOLUTE. I have 2 questions: 1. Which platform should I use? I noticed there are 3 supported platforms: SNP_250K_STY, SNP_6.0 (default), Illumina_WES. None of them is WGS, so whi ...
absolute next-gen tumor purity ploidy written 7 months ago by shiyang9320

Latest awards to shiyang93

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1230 users visited in the last hour