User: Pascal

gravatar for Pascal
Pascal250
Reputation:
250
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Trusted
Location:
European Union
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Google Scholar Page
Last seen:
1 day, 23 hours ago
Joined:
5 years, 7 months ago
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p*************@gmail.com

Posts by Pascal

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... I am using clumpify on HiSeq4000 data. As recommended, I increased dupedist to 2500 because of patterned flow cells. However, I get exclusively optical duplicates using this option: dupedist=2500 dedupe=t optical=t Gives the same output as: dupedist=2500 dedupe=t Any ideas? All optical ...
written 5 months ago by Pascal250
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Job: Senior Bionformatics Officer - Breast Cancer Research - ICR London, UK
... We currently have a vacancy for a highly motivated Senior Bioinformatics Officer to provide support for our ongoing molecular profiling and Next-Generation Sequencing projects within the Endocrinology Team, and to build on existing collaborations with other groups within the UK and internationally. ...
jobs written 24 months ago by Pascal250
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Comment: C: Is It Possible To Convert Illumina Genotype Data Into Affymetrix-Like Format?
... This is a very old thread, but maybe you could share your experiences. I am having the same problem (ASCAT and OncoSNP give me quite different results for some samples) and wonder if ABSOLUTE gave you better results. ...
written 2.0 years ago by Pascal250
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Answer: A: Issues with DiffBind
... Hi Val, Make sure your header in the sample sheet is right. Looks like your Peak column cannot be found. Here is how my header looks like: SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks,PeakCaller,ControlID Pascal ...
written 2.3 years ago by Pascal250
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Comment: C: VarScan output different when choosing VCF and variant missing?
... No, I wasn't able to track down what happens there. ...
written 2.3 years ago by Pascal250
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Answer: A: genome music bmr cal-covg
... Not quite sure, but I think only the tumor bam is required. Format is  ID<TAB>Another ID<TAB>path/to/Tumor.bam ...
written 2.6 years ago by Pascal250
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Comment: C: VarScan output different when choosing VCF and variant missing?
... Just tried version 2.3.1. With both options 1 somatic mutation is reported and both output files contain this mutation. ...
written 2.7 years ago by Pascal250
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VarScan output different when choosing VCF and variant missing?
... Hi, I am using VarScan version 2.3.7 for variant calling in my tumour samples. Depending if I choose VCF as output I seem to get different results. Here is an example on a specific position where I am expecting to find one somatic mutation, but get none in both cases: java -jar VarScan.v2.3.7.jar ...
variant calling varscan vcf exome-seq written 2.7 years ago by Pascal250
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Answer: A: Got Error When Using Exomecnv To Call Loh
... Hi Conan, I got the same error. After removing extra chromosomes (I had GLXXXX included) everything worked fine. Pascal ...
written 2.7 years ago by Pascal250
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SNPeff result interpretation
... Hi, I am using SNPeff to annotate my somatic mutations. That works well, however I am not sure how to interpret the result. Below is the annotation added to the INFO field by SNPeff. I get many times the exact same annotation, except the Rank is different. All I found in the documentation is that t ...
wes snpeff variant annotation cancer written 2.7 years ago by Pascal250

Latest awards to Pascal

Popular Question 11 weeks ago, created a question with more than 1,000 views. For SNPeff result interpretation
Popular Question 19 months ago, created a question with more than 1,000 views. For VarScan output different when choosing VCF and variant missing?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Music Analysis Workflow
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Re
Good Question 2.8 years ago, asked a question that was upvoted at least 5 times. For Music Analysis Workflow
Appreciated 3.4 years ago, created a post with more than 5 votes. For Music Analysis Workflow
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: How To Determine If Library Is Strand-Specific
Student 3.6 years ago, asked a question with at least 3 up-votes. For Music Analysis Workflow
Supporter 3.6 years ago, voted at least 25 times.
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Re

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