User: Travis

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Travis2.8k
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4 years, 6 months ago
Joined:
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Posts by Travis

<prev • 241 results • page 1 of 25 • next >
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Answer: A: How To Identify Targets Of A Transcription Factor ?
... Old question but still relevant and think this resource answers it: http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm ...
written 5.1 years ago by Travis2.8k
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Comment: C: Comparing Rpkms For One Test Sample Vs Multiple Controls
... I had assumed it would not be safe to take raw counts from different sources/centers and attempt differential expression analysis. Do both DESeq and edgeR attempt to correct for issues like differences in sequencing depth? ...
written 5.1 years ago by Travis2.8k
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Comparing Rpkms For One Test Sample Vs Multiple Controls
... Hi all, I have RPKM values for a single sample (lung adenocarcinoma) and wish to compare it to RPKM values for a group of controls (50 TCGA normal lung samples). Bearing in mind the one to many nature of the analysis, and RPKMs being the starting point, can someone recommend the best method/softw ...
differential-expression next-gen rna-seq written 5.1 years ago by Travis2.8k • updated 5.1 years ago by Hayssam250
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Comment: C: Somatic Sniper Producing Slightly Different Call Numbers Depending On Whether Du
... We are currently using 3 callers and doing extensive downstream filtering using automated and manual techniques so I am not necessarily taking the SS output as gospel truth. I guess I'm just curious to know why this happens. ...
written 5.9 years ago by Travis2.8k
7
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Answer: A: Database Of Tumor Suppressors And/Or Oncogenes
... I realize this is an old thread but still a very relevant question. The following resource ticks most boxes for tumor suppressor genes. It is a recent (NAR) published database resource, complete with literature evidence, downloadable data and a number of nice web-based resources like the ability t ...
written 5.9 years ago by Travis2.8k
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Comment: C: Database Of Human Structural Variants Enabling Vcf File Creation
... Apologies - I have edited the question to include "The end goal is to assess a range of SV detection tools using an unbiased, mutated dataset". Since the 1000G VCFs are largely unvalidated and based on some of the software I would like to test, it doesn't satisfy the well-validated/unbiased criteri ...
written 6.4 years ago by Travis2.8k
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Database Of Human Structural Variants Enabling Vcf File Creation
... Hi all, I am trying to get hold of or create a VCF format file containing known, well validated human structural variants in order to introduce them into a reference genome. The end goal is to assess a range of SV detection tools using an unbiased, mutated dataset. Is anyone aware of a human SV ...
vcf sv next-gen written 6.4 years ago by Travis2.8k • updated 6.4 years ago by deanna.church1.1k
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Comment: C: Trying To Understand A Simple Perl Vs Python Vs Sed Benchmark
... Firstly there is more to the problem than I stated in my original question. Secondly, the solution needs to be useable by people with no bioinformatics training. ...
written 6.6 years ago by Travis2.8k
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Comment: C: Trying To Understand A Simple Perl Vs Python Vs Sed Benchmark
... I'm running on a virtual machine witrh limited memory so this particular approach ground the machine to a halt! ...
written 6.6 years ago by Travis2.8k
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Comment: C: Trying To Understand A Simple Perl Vs Python Vs Sed Benchmark
... Thanks Heng. Are there particular problems that Python performs better on? ...
written 6.6 years ago by Travis2.8k

Latest awards to Travis

Popular Question 4.5 years ago, created a question with more than 1,000 views. For Bwa Aln For Snp/Indel Discovery With Paired End 100Bp Human Dna Reads
Good Question 4.5 years ago, asked a question that was upvoted at least 5 times. For Snp Indel Discovery - Critique A Proposed Workflow
Student 5.0 years ago, asked a question with at least 3 up-votes. For Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
Student 5.0 years ago, asked a question with at least 3 up-votes. For Variation & Genotype Calling From Ngs Data - Per Sample Or Multi Sample?
Student 5.0 years ago, asked a question with at least 3 up-votes. For Snp Indel Discovery - Critique A Proposed Workflow
Student 5.0 years ago, asked a question with at least 3 up-votes. For Introducing Known Mutations (From A Vcf) Into A Fasta File
Student 5.0 years ago, asked a question with at least 3 up-votes. For Genomic Alignment And Snp/Indel Calling - My First Ever "Pipeline"
Student 5.0 years ago, asked a question with at least 3 up-votes. For Thoughts On Galaxy For Next Generation Sequence Data Analysis
Student 5.0 years ago, asked a question with at least 3 up-votes. For Defining Your Reference Genome From Ucsc For Human Ngs Studies
Student 5.0 years ago, asked a question with at least 3 up-votes. For Using Cufflinks For Rna-Seq Without Tophat/Bowtie.
Student 5.0 years ago, asked a question with at least 3 up-votes. For Differential Expression Analysis Theory/Tutorial For The Statistics Layman
Student 5.0 years ago, asked a question with at least 3 up-votes. For Next Gen Sequencing Indel Realignment With The Genome Analysis Toolkit (Gatk)
Supporter 5.0 years ago, voted at least 25 times.
Student 5.0 years ago, asked a question with at least 3 up-votes. For Picking A Programming Language And Where To Begin
Voter 5.0 years ago, voted more than 100 times.
Student 5.0 years ago, asked a question with at least 3 up-votes. For Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
Centurion 5.0 years ago, created 100 posts.
Student 5.0 years ago, asked a question with at least 3 up-votes. For Links To Good Next Gen Sequence Analysis Training Courses And Centres
Guru 5.0 years ago, received more than 100 upvotes.
Student 5.0 years ago, asked a question with at least 3 up-votes. For How Do You Do Local Realignment Around Indels For Exome Sequencing?
Student 5.0 years ago, asked a question with at least 3 up-votes. For Is Anyone Familiar With Knome And Their Kgap Software?
Student 5.0 years ago, asked a question with at least 3 up-votes. For Exon Arrays Vs Rna-Seq
Student 5.0 years ago, asked a question with at least 3 up-votes. For Using Simngs To Generate Reads
Student 5.0 years ago, asked a question with at least 3 up-votes. For Trying To Understand A Simple Perl Vs Python Vs Sed Benchmark
Student 5.0 years ago, asked a question with at least 3 up-votes. For Benchmarking Read Alignment And Variant-Calling Algorithms (For Dummies)

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