User: Travis

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Travis2.8k
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Posts by Travis

<prev • 245 results • page 1 of 25 • next >
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Answer: A: Tophat2/Bowtie failing to align some examples of partial intron retention / exon
... Working in a core facility with high throughput, reassessment of underlying aligners etc on a per project basis is an impossibility. Furthermore we have recently observed Tophat to be much better at detecting fusion transcripts than STAR in our samples so I wouldn't be replacing it without extende ...
written 5 months ago by Travis2.8k
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Comment: C: Tophat2/Bowtie failing to align some examples of partial intron retention / exon
... As mentioned to the previous user, Tophat is currently ingrained in several of our pipelines and switching up aligners completely is non-trivial, hence the desire to attempt fine-tuning the Tophat alignments or at least understand the reason behind the missed event. Critically assessing alignment r ...
written 5 months ago by Travis2.8k
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Comment: C: Tophat2/Bowtie failing to align some examples of partial intron retention / exon
... We tried STAR aligner and it detected both events. Problem is that Bowtie is ingrained in some of our pipelines so I was hoping to figure out whether it could be parameterized to make the calls. ...
written 5 months ago by Travis2.8k
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Tophat2/Bowtie failing to align some examples of partial intron retention / exon loss
... Hi all, We have discovered a couple of examples where variants were predicted to affect normal splicing but Tophat2/Bowtie failed to identify the effect on splicing within the RNA-Seq alignments. Specifically we have two recent examples, one of which resulted in a 2bp loss at the 5 prime end of a ...
alignment rna-seq written 5 months ago by Travis2.8k • updated 5 months ago by Charles Warden6.9k
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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 5.6 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 5.6 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 5.6 years ago by Travis2.8k • updated 5.6 years ago by Hayssam270
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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 6.4 years ago by Travis2.8k
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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 6.4 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 6.9 years ago by Travis2.8k

Latest awards to Travis

Appreciated 5.0 years ago, created a post with more than 5 votes. For A: Conference On Statistics Of Ngs Data
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Great Question 5.0 years ago, created a question with more than 5,000 views. For Exon Arrays Vs Rna-Seq
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Great Question 5.0 years ago, created a question with more than 5,000 views. For Introducing Known Mutations (From A Vcf) Into A Fasta File
Great Question 5.0 years ago, created a question with more than 5,000 views. For Thoughts On Galaxy For Next Generation Sequence Data Analysis
Great Question 5.0 years ago, created a question with more than 5,000 views. For Single Gene Sequencing And Mutation Analysis
Great Question 5.0 years ago, created a question with more than 5,000 views. For Trying To Understand A Simple Perl Vs Python Vs Sed Benchmark
Librarian 5.0 years ago, created a post with more than 10 bookmarks. For Links To Good Next Gen Sequence Analysis Training Courses And Centres
Librarian 5.0 years ago, created a post with more than 10 bookmarks. For Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
Prophet 5.0 years ago, created a post with more than 20 followers. For Links To Good Next Gen Sequence Analysis Training Courses And Centres
Prophet 5.0 years ago, created a post with more than 20 followers. For Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
Good Question 5.0 years ago, asked a question that was upvoted at least 5 times. For Links To Good Next Gen Sequence Analysis Training Courses And Centres
Good Question 5.0 years ago, asked a question that was upvoted at least 5 times. For Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
Good Question 5.0 years ago, asked a question that was upvoted at least 5 times. For Snp Indel Discovery - Critique A Proposed Workflow
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics Career Survey 2011/2012
Epic Question 5.0 years ago, created a question with more than 10,000 views. For Links To Good Next Gen Sequence Analysis Training Courses And Centres
Epic Question 5.0 years ago, created a question with more than 10,000 views. For Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
Epic Question 5.0 years ago, created a question with more than 10,000 views. For How To Build A Basic Rna-Seq Pipeline
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: Bioinformatics Career Survey 2011/2012

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