Moderator: Anton Nekrutenko

gravatar for Anton Nekrutenko
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Penn State
Website:
http://nekrut.bx.psu.edu/
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Joined:
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Posts by Anton Nekrutenko

<prev • 164 results • page 1 of 17 • next >
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Answer: A: TopHat tool missing?
... We deprecated TopHat in favor of HISAT2 - a much more efficient spliced aligner from the same group. It can be used as a drop-in replacement in your previous TopHat analyses. There are two ways is which you can perform downstream analyses: - you can continue using CuffLinks - you can use a new tr ...
written 6 months ago by Anton Nekrutenko1.7k • updated 6 months ago by Mo Heydarian790
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Answer: A: Tophat vs HISAT
... HiSat (in particular HiSat2 that is currently on Galaxy) is the next generation of spliced aligner from the same group that have developed TopHat. It is MUCH faster and you can use its output for your old pipeline as well. This tutorial (https://galaxyproject.org/tutorials/rb_rnaseq/#read-mapping) e ...
written 6 months ago by Anton Nekrutenko1.7k
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Comment: C: Error message after running FreeBayes
... Naive Variant Caller is ... naive. It just tabulates the number of differences. But since calling variants in RNAseq does not necessary follow diplod assumption it may work for you (FreeBayes also has pooled continuous function for such cases). It is the **NGS: Variant Analysis** section on the tool ...
written 8 months ago by Anton Nekrutenko1.7k
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Answer: A: Question about Hisat2 + htseq-count
... My guess if that since htseq-count uses annotation for counting extensions beyond feature coordinates should not affect the result. ...
written 8 months ago by Anton Nekrutenko1.7k
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Answer: A: Environment variables in label field of output block?
... Can you tell me why you need to do this? Perhaps there a simpler solution ...
written 8 months ago by Anton Nekrutenko1.7k
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Answer: A: Error message after running FreeBayes
... Federico B: HISAT is a spliced mapper and it is possible that FreeBayes does not like BAM files generated by HISAT. Can you try Naive Varinat Caller instead and see if you will be getting valid VCF. ...
written 8 months ago by Anton Nekrutenko1.7k
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Comment: C: Missing fields in Picard 'Collect Alignment Summary Metrics' tool(s)?
... Guy: For backward compatibility there are TWO versions of picard at usegalaxy.org (the old version will soon be hidden). The one you want to use is in "NGS: Picard" category (not "NGS: Picard (beta)").  Simply replace the old version of the tool with the new one in your workflow. Let me know if thi ...
written 2.7 years ago by Anton Nekrutenko1.7k
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Answer: A: uploading .gz files
... You cannot upload large files through the browser due to inherent browser limitations. Use ftp upload instead as shown here https://vimeo.com/120972739     ...
written 2.7 years ago by Anton Nekrutenko1.7k
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Answer: A: installation toolshed errors - realigner target creator
... Pieter: While we were planning on supporting GATK.  However since they moved to a closed source model we are not planning on supporting GATK. Functionality provided by FreeBayes (which includes leftalign) should be quite comparable to GATK. a. ...
written 2.7 years ago by Anton Nekrutenko1.7k
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Answer: A: Fastq joiner and sequencing reads previously submitted to a quality based trimmi
... One of the assumptions made by the joiner is that the sequences are of the same length. Why are you trying to join sequences? ...
written 2.7 years ago by Anton Nekrutenko1.7k

Latest awards to Anton Nekrutenko

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Creating a Workflow for Variant Detection for 200 samples
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: TopHat tool missing?
Appreciated 6 months ago, created a post with more than 5 votes. For A: TopHat tool missing?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Creating a Workflow for Variant Detection for 200 samples
Centurion 4.7 years ago, created 100 posts.

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