User: Dawe

gravatar for Dawe
Dawe220
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220
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Location:
Milan
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http://sites.google.co...
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1 year ago
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7 years, 1 month ago
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Posts by Dawe

<prev • 14 results • page 1 of 2 • next >
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Comment: C: 1000 Genomes exomes as controls
... I have now the very same problem. Did you find any valuable resource? I'm reading the original paper by Neale trying to implement c-alpha test based on allele counts found in ExAC data. In principle you won't need individual genotypes, only allele counts. Unfortunately the methodology described has ...
written 13 months ago by Dawe220
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Using offsets in edgeR to correct GC content
... Hi all, I'm performing some differential analysis with edgeR and I need to take into account GC content in my regions. From edgeR manual I see I should set GC percentage as "offset" in linear model. Unfortunately there is very little documentation about this, so I need some hint. Offsets can be pa ...
R gc linear models edger written 18 months ago by Dawe220 • updated 15 months ago by javiergutierreza30
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Job: Computational biologist @ Center for Translational Genomics and Bioinformatics (Milan)
... The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a profile in collaboration with the Pathogenesis and Therapy of Primary Immunodeficiencies unit at SR-TIGET. The role will involve: - analysis of NGS data, with a focus on Exome Sequencing and Targeted Resequencing data for ...
immunodeficiency exome sequencing job gene therapy written 19 months ago by Dawe220
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Job: Computational biologist, analysis oriented, Center of Translational Genomics and Bioinformatics, Milan, Italy
... The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a profile to reinforce the core team responsible for analysis of omics data generated by the Genomics Unit. The role will involve: analysis of NGS data, including the integration of different data sources, in collaboration ...
epigenome genomics rna-seq job written 2.6 years ago by Dawe220 • updated 2.6 years ago by Istvan Albert ♦♦ 75k
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Job: Computational biologist, programming oriented, Center of Translational Genomics and Bioinformatics, Milan, Italy
... The Center of Translational Genomics and Bioinformatics (CTGB) is seeking a motivated individual to reinforce the development team responsible for original analytical tools and platforms. The role will involve: development of libraries and tools for the analysis of sequencing data participat ...
core job genomics programming written 2.6 years ago by Dawe220 • updated 2.6 years ago by Istvan Albert ♦♦ 75k
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Filtering Pindel Results
... Dear all, I've been running pindel on a set of BAM files. I've then converted files to vcf using pindel2vcf utility. Which rules would apply to tell if a variant is likely to be present in a sample (or sample set)? I mean, if I have a variant with 10 reads in one sample and 2 reads in another (both ...
filter coverage pindel written 4.6 years ago by Dawe220 • updated 4.6 years ago by liangkaiye250
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Answer: A: Cross-Correlation On Chip-Seq Like Data?
... I'm kind of interested in this topic. I'm developer of a package for digital signal processing of quantitative genomic data (such as ChIP-seq). Cross-correlation is something I was implementing too, although I had some issues with the border effect, and also I was not sure xcorr is a proper measure ...
written 6.7 years ago by Dawe220
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Answer: A: Proteolysis Of A Protein Sequence
... There should be a plenty of such scripts. BTW, you can look at function "cleave" (line 764) in this source http://code.google.com/p/nsilk/source/browse/trunk/xllib/sequence.py?r=143 Nsilk is a python tool to spot protein-protein interactions, but that function will predict peptides from a sequence. ...
written 7.0 years ago by Dawe220
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Answer: A: How To Combine Multiple Wig/Bigwig Files Into One
... If you have multiple wig files (and MACS wig are gzipped) you should concatenate: zcat *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig If you have only one file (and macs14 allows this) you can directly go with wigToBigWig -clip stdin chromsizes.tab output.bigwig As recent wigToBi ...
written 7.0 years ago by Dawe220
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Comment: C: Evidences For Choice Of Ngs Instrument
... I also have experience with Illumina, but now I have to justify why I would need the 100bp-PE capability of the HiSeq2k. I mean, in terms of precision, Illumina relies on the high number and the longer (paired) reads (up to 100/150 bp in paired ends), Solid relies on its chemistry... in the end whic ...
written 7.1 years ago by Dawe220

Latest awards to Dawe

Popular Question 13 months ago, created a question with more than 1,000 views. For Filtering Pindel Results
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Filtering Pindel Results
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Cross-Correlation On Chip-Seq Like Data?
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: What Parameters Do You Use With Findpeaks For Chip Seq Peak Calling?
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: How To Combine Multiple Wig/Bigwig Files Into One
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Open Source Mass Spec Search Engines?
Student 4.6 years ago, asked a question with at least 3 up-votes. For Filtering Pindel Results

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