User: KS

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KS370
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Posts by KS

<prev • 24 results • page 1 of 3 • next >
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Answer: A: SNPTEST v2.5.4 for GWAS analysis
... Hi, I am facing same problem, were you able to figure it out. Also did you run this method newml on chromosome X data? Thanks ...
written 5 weeks ago by KS370
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X-chromsome association testing
... I recently started working association testing for chromosome X, I have imputed data from michigan imputation server. I am working to do association testing using SNPTEST/PLINK. Can anyone share there experiences using these two softwares ...
plink snp snptest written 3 months ago by KS370 • updated 5 weeks ago by Biostar ♦♦ 20
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How To Filter Fusions When Using Tophat2 In Galaxy
... Hi All, I am trying to detect fusions using tophat2 in Galaxy and tophat2 generated fusion file with out any errors. My question is how to filter those fusions using fusion-post. does Galaxy have tophat fusion-post. Any kind of help is greatly appreciated Thanks Suz ...
tophat2 galaxy written 7.2 years ago by KS370 • updated 7.2 years ago by Istvan Albert ♦♦ 84k
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Mutect Vcf Output
... Hello Everyone, I just started using muTect to detect somatic mutations in matching tumor normal bam files. I would like to output in VCF format for downstream annovar annotation process. Can anyone suggest how to output MuTect in VCF format Below is the command I am using currently: java -Xmx2g ...
vcf written 7.3 years ago by KS370 • updated 7.3 years ago by henryvuong780
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Looking For Reasons Of Why The Results Of A Tophat Fusion Post Is Empty
... Hello Everyone, I ran tophat-2.7 on the example data with --fusion-search , it ran successfully and produced the following output files: accepted hits.bam, deletions.bed, insertions.bed, junctions.bed, fusions.out I am trying to run tophat-fusion-post, after I run it, the output is empty. Can anyo ...
tophat fusion written 7.3 years ago by KS370 • updated 6.0 years ago by Paul1.4k
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Aligning Reads To Specific Chromosome Using Bwa
... Hello Everyone, I have whole genome illumina paired end reads and I want to align my reads to specific chromosome (chr 21) using BWA. I was thinking of aligning the entire reads to fasta file of the human chromosome 21. Is this the appropriate way to solve my problem or is there any specific comm ...
paired-end bwa written 7.4 years ago by KS370 • updated 7.4 years ago by Chris Miller21k
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Answer: A: Can Tophat Be Used For Mapping Dna-Seq (Whole Genome) Data
... Thanks for the info. It really helped me a lot ...
written 7.4 years ago by KS370
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Can Tophat Be Used For Mapping Dna-Seq (Whole Genome) Data
... Hello, Can tophat be used for mapping DNA-Seq (Whole genome) Data. Basically, while reading through the articles most of them mentioned usage of Tophat for RNA-seq data and BWA or Bowtie for DNA-Seq (Whole Genome) mapping. Is it ok to use tophat for mapping of DNA-Seq reads? Thanks Suz ...
tophat bwa written 7.4 years ago by KS370 • updated 4.0 years ago by ghv80
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Why Do I Get The Tophat Fusion Error: --Fusion-Search Not Recognized
... Hey guys, I am trying to find fusion junctions using tophat-fusion I downloaded and installed tophat-fusion. But I am getting an error tophat-fusion: option --fusion-search not recognized. Here is the command I followed: tophat -o tophat_MCF7 -p 8 --fusion-search --bowtie1 --no-coverage-searc ...
tophat2 written 7.4 years ago by KS370 • updated 7.4 years ago by Istvan Albert ♦♦ 84k
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How To Find Snps And Mutations In Galaxy
... HI, I have RNA-Seq data from cancer tumor sample and two reference normal sample and I want to find out SNPs and mutations in my data and the only available sources for me to do analysis is the Galaxy. I did the alignment using tophat, ran pileup on tophats output .bam files for all the four sampl ...
galaxy rna-seq snp written 7.6 years ago by KS370

Latest awards to KS

Appreciated 7.2 years ago, created a post with more than 5 votes. For Gene Fusion Detection: Rna-Seq Data
Appreciated 7.2 years ago, created a post with more than 5 votes. For Bioinformatics Training On Next-Generation Sequencing Data
Great Question 7.2 years ago, created a question with more than 5,000 views. For Gene Fusion Detection: Rna-Seq Data
Great Question 7.2 years ago, created a question with more than 5,000 views. For Aligning Reads To Specific Chromosome Using Bwa
Great Question 7.2 years ago, created a question with more than 5,000 views. For Cufflinks And Cuffdiff Fpkm Values In Galaxy
Great Question 7.2 years ago, created a question with more than 5,000 views. For Bioinformatics Training On Next-Generation Sequencing Data
Great Question 7.2 years ago, created a question with more than 5,000 views. For Mutect Vcf Output
Librarian 7.2 years ago, created a post with more than 10 bookmarks. For Gene Fusion Detection: Rna-Seq Data
Prophet 7.2 years ago, created a post with more than 20 followers. For Gene Fusion Detection: Rna-Seq Data
Good Question 7.2 years ago, asked a question that was upvoted at least 5 times. For Gene Fusion Detection: Rna-Seq Data
Good Question 7.2 years ago, asked a question that was upvoted at least 5 times. For Bioinformatics Training On Next-Generation Sequencing Data
Epic Question 7.2 years ago, created a question with more than 10,000 views. For Gene Fusion Detection: Rna-Seq Data
Epic Question 7.2 years ago, created a question with more than 10,000 views. For Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Cnv Mutation Analysis Rna-Seq
Popular Question 7.2 years ago, created a question with more than 1,000 views. For How To Filter Fusions When Using Tophat2 In Galaxy
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Whole Genome Analysis Using Galaxy
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Galaxy Tophat
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Can Tophat Be Used For Mapping Dna-Seq (Whole Genome) Data
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Why Do I Get The Tophat Fusion Error: --Fusion-Search Not Recognized
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Gene Fusion Detection: Rna-Seq Data
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Homology Modeling
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Aligning Reads To Specific Chromosome Using Bwa
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Tophat Installation
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Ligand Binding Cavities & Docking
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Cufflinks And Cuffdiff Fpkm Values In Galaxy

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