User: KS

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KS310
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3 years, 9 months ago
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Posts by KS

<prev • 22 results • page 1 of 3 • next >
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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 3.8 years ago by KS310 • updated 3.8 years ago by Istvan Albert ♦♦ 69k
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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 3.9 years ago by KS310 • updated 3.9 years ago by henryvuong640
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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 4.0 years ago by KS310 • updated 2.6 years ago by Paul490
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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 4.0 years ago by KS310 • updated 4.0 years ago by Chris Miller17k
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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 4.0 years ago by KS310
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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 4.0 years ago by KS310 • updated 7 months 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 4.0 years ago by KS310 • updated 4.0 years ago by Istvan Albert ♦♦ 69k
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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 4.2 years ago by KS310
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Comment: C: Cnv Mutation Analysis Rna-Seq
... Yes, I did use Tophat in Galaxy for alignment.. ...
written 4.2 years ago by KS310
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Cnv Mutation Analysis Rna-Seq
... Hello, I am analyzing RNA-Seq data of cancer patients using Galaxy Tools. Could any one let me know how to find out CNS or mutations or any indel variants? Thanks a lot Kat ...
mutation rna-seq cnv written 4.2 years ago by KS310 • updated 14 months ago by Biostar ♦♦ 10

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