User: Christian

gravatar for Christian
Christian2.4k
Reputation:
2,390
Status:
Trusted
Location:
Vienna
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Google Scholar Page
Last seen:
11 hours ago
Joined:
5 years, 7 months ago
Email:
f**************@gmail.com

Posts by Christian

<prev • 222 results • page 1 of 23 • next >
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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 19 days ago by Christian2.4k
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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 5 weeks ago by Christian2.4k
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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 8 weeks ago by Christian2.4k
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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 3 months ago by Christian2.4k
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Comment: C: Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
... Yes, the position has not been filled yet. ...
written 4 months ago by Christian2.4k
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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 5 months ago by Christian2.4k
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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 6 months ago by Christian2.4k
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Comment: C: Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
... The research synopsis was a mistake and removed. This is primarily a service-based position and MSc with extensive NGS experience are encouraged to apply. ...
written 6 months ago by Christian2.4k
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Comment: C: Presence of both forward and reverse motifs in transcription factor binding site
... Many TFs bind DNA as homodimer, which in general explains this observation. However, this requires the binding motif to be palindromic. This is not true for your example here, but you could check the others. ...
written 7 months ago by Christian2.4k
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Comment: C: Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
... Start date is September to November 2016. Applications are welcome until the position is filled, which I expect will be the case 6 to 8 weeks from now. If you finish your PhD November that's a bit late for us, but then a good candidate is worth waiting for. So you might try. ...
written 7 months ago by Christian2.4k

Latest awards to Christian

Popular Question 17 days ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How To Correctly Classify Gene Families?
Prophet 4 months ago, created a post with more than 20 followers. For Are we facing a bioinformatician shortage?
Prophet 5 months ago, created a post with more than 20 followers. For Which software do you use for RNA-seq data quality control?
Popular Question 5 months ago, created a question with more than 1,000 views. For Does Fasta Produce A Local Or Global Alignment?
Great Question 7 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 8 months ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Student 9 months ago, asked a question with at least 3 up-votes. For Program to prioritize silent SNVs?
Great Question 9 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 10 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 11 months ago, created a question with more than 1,000 views. For How To Compute A Local Multiple Protein Sequence Alignment?
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Detecting Polyploidy Using An Assembly
Teacher 12 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 13 months ago, created a question with more than 1,000 views. For Acceptable "Percentage Of Usable Bases On Target" In Exome Sequencing Experiment
Teacher 13 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 14 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 15 months ago, created a question with more than 1,000 views. For Acceptable "Percentage Of Usable Bases On Target" In Exome Sequencing Experiment
Teacher 15 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 15 months ago, created a question with more than 1,000 views. For Acceptable "Percentage Of Usable Bases On Target" In Exome Sequencing Experiment
Appreciated 16 months ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Appreciated 16 months ago, created a post with more than 5 votes. For A: Visualizing Pairwise Distance Between A Group Of Sequences
Prophet 16 months ago, created a post with more than 20 followers. For Which software do you use for RNA-seq data quality control?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Renaming All Files In A Directory With A Perl Script
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Detecting Polyploidy Using An Assembly

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