User: Christian

gravatar for Christian
Christian2.5k
Reputation:
2,530
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Location:
Vienna
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Last seen:
2 months, 1 week ago
Joined:
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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 10 weeks ago by Christian2.5k
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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 3 months ago by Christian2.5k
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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 5 months ago by Christian2.5k
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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 6 months ago by Christian2.5k
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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 7 months ago by Christian2.5k
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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 7 months ago by Christian2.5k
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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 9 months ago by Christian2.5k
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Comment: C: Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
... Yes, the position has not been filled yet. ...
written 10 months ago by Christian2.5k
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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 11 months ago by Christian2.5k
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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 11 months ago by Christian2.5k

Latest awards to Christian

Appreciated 3 months ago, created a post with more than 5 votes. For A: Detecting Polyploidy Using An Assembly
Appreciated 5 months ago, created a post with more than 5 votes. For A: Detecting Polyploidy Using An Assembly
Popular Question 5 months ago, created a question with more than 1,000 views. For Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
Popular Question 5 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Popular Question 5 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Teacher 5 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 6 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How To Correctly Classify Gene Families?
Prophet 10 months ago, created a post with more than 20 followers. For Are we facing a bioinformatician shortage?
Prophet 11 months ago, created a post with more than 20 followers. For Which software do you use for RNA-seq data quality control?
Popular Question 11 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Great Question 12 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?
Appreciated 13 months ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Student 15 months ago, asked a question with at least 3 up-votes. For Program to prioritize silent SNVs?
Great Question 15 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?
Teacher 16 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 17 months ago, created a question with more than 1,000 views. For How To Compute A Local Multiple Protein Sequence Alignment?
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Detecting Polyploidy Using An Assembly
Teacher 18 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 19 months ago, created a question with more than 1,000 views. For Acceptable "Percentage Of Usable Bases On Target" In Exome Sequencing Experiment
Teacher 19 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 20 months ago, created a question with more than 1,000 views. For Acceptable "Percentage Of Usable Bases On Target" In Exome Sequencing Experiment
Popular Question 20 months ago, created a question with more than 1,000 views. For Acceptable "Percentage Of Usable Bases On Target" In Exome Sequencing Experiment

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