User: Christian

gravatar for Christian
Christian2.7k
Reputation:
2,700
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Location:
Cambridge, US
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Last seen:
10 months, 2 weeks ago
Joined:
7 years, 3 months ago
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Posts by Christian

<prev • 225 results • page 1 of 23 • next >
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Answer: A: CRISPR off-target effects causing unexpected mutations - good science or media h
... Wrong control (different mouse strain) and tiny sample size. Waiting for proper study here (which is overdue btw). ...
written 17 months ago by Christian2.7k
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Comment: C: DESeq2: Find differentially expressed genes specific to one condition
... Unfortunately not. I went ahead with the set-overlap solution, although I am still not fully satisfied with it from a statistical point of view. EDIT: should have been a comment to the previous answer, not a reply to this comment. ...
written 18 months ago by Christian2.7k
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Answer: A: Confusion : Why and how does a nucleotide in Reference Genome is differenet from
... Most likely reference genome and RefSeq represent different alleles. Less likely but possible are sequencing errors and RNA editing. ...
written 20 months ago by Christian2.7k
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Answer: A: Aligning paired end fastq files dumped from SRA
... The following command worked for me: cat sra.fq | perl -ne 's/\.([12]) /\/$1 /; print $_' > sra.fix.fq ...
written 21 months ago by Christian2.7k
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Comment: C: Variant Effect Predictor parameters for custom gff and fasta
... [CooVar][1] was developed for annotating non-standard genomes. The paper contains an in-depth comparison with VEP results. (Disclaimer: I'm co-author of this paper). [1]: http://link.springer.com/article/10.1186/1756-0500-5-615 ...
written 22 months ago by Christian2.7k
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Comment: C: run our pipeline on TCGA data
... The Cancer Genomics Cloud (CGC) from SevenBridges allows you to bring your own custom tools/pipeline to the TCGA data using a SDK. In addition, pilot funds from the NCI are available to cover (at least partially) for the compute cost. Direct access to user buckets is also possible via the Volumes AP ...
written 22 months ago by Christian2.7k
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Comment: C: Use a workflow management tool to manage your computational pipelines
... Another really good place to start: https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems ...
written 2.0 years ago by Christian2.7k
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Comment: C: Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
... Yes, the position has not been filled yet. ...
written 2.1 years ago by Christian2.7k
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Comment: C: Recommended tools for positional gene enrichment (PGE) analysis?
... I haven't looked for it, because the Perl script works well and I am still using it in my analysis pipelines (in addition to GSEA with MSigDB positional gene sets). ...
written 2.2 years ago by Christian2.7k
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Comment: C: What's the recommended graduate educational path for a fullstack developer to tr
... Check out the bioinformatics subreddit. They have a lot of carreer-related discussions and you might get some useful advice there as well. Good luck! ...
written 2.2 years ago by Christian2.7k

Latest awards to Christian

Epic Question 11 months ago, created a question with more than 10,000 views. For Which software do you use for RNA-seq data quality control?
Popular Question 17 months ago, created a question with more than 1,000 views. For Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
Great Question 17 months ago, created a question with more than 5,000 views. For Are we tricking ourselves with batch effect correction?
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Use a workflow management tool to manage your computational pipelines
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Music Proximity Analysis Mutation Diagrams
Great Question 17 months ago, created a question with more than 5,000 views. For Anyone Has A Working Example On How To Run BROAD's ABSOLUTE On Exome Sequencing Data?
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For Is the DAVID knowledgebase not updated any more?
Appreciated 18 months ago, created a post with more than 5 votes. For A: Detecting Polyploidy Using An Assembly
Appreciated 20 months ago, created a post with more than 5 votes. For A: Detecting Polyploidy Using An Assembly
Popular Question 20 months ago, created a question with more than 1,000 views. For Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
Popular Question 20 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Popular Question 20 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Renaming All Files In A Directory With A Perl Script
Popular Question 21 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Appreciated 22 months ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: How To Correctly Classify Gene Families?
Prophet 2.1 years ago, created a post with more than 20 followers. For Are we facing a bioinformatician shortage?
Prophet 2.2 years ago, created a post with more than 20 followers. For Which software do you use for RNA-seq data quality control?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Great Question 2.3 years ago, created a question with more than 5,000 views. For Anyone Has A Working Example On How To Run BROAD's ABSOLUTE On Exome Sequencing Data?
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Student 2.5 years ago, asked a question with at least 3 up-votes. For Program to prioritize silent SNVs?
Great Question 2.5 years ago, created a question with more than 5,000 views. For Anyone Has A Working Example On How To Run BROAD's ABSOLUTE On Exome Sequencing Data?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Renaming All Files In A Directory With A Perl Script

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