Moderator: Anton Nekrutenko

gravatar for Anton Nekrutenko
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Posts by Anton Nekrutenko

<prev • 167 results • page 1 of 17 • next >
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Answer: A: usegalaxy build snpEff database via genbank
... Yes, it is the result of fragmented genome. We will try to modify SnpEff build to accept GFF in the next few days. ...
written 7 weeks ago by Anton Nekrutenko1.7k
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Answer: A: usegalaxy build snpEff database via genbank
... This seems like SnpEff issue. If I understand correctly, Salmon genome assembly is highly fragmented and so the same gene can be split between several scaffolds. This is likely what is happening here. Let me take a closer look. ...
written 7 weeks ago by Anton Nekrutenko1.7k
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Answer: A: usegalaxy build snpEff database via genbank
... Have you tried to create the DB from entire Salmon genome: https://www.ncbi.nlm.nih.gov/nuccore/925216783?report=genbank ...
written 7 weeks ago by Anton Nekrutenko1.7k
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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 14 months ago by Anton Nekrutenko1.7k • updated 14 months ago by Mo Heydarian800
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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 14 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 16 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 16 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 16 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 16 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 3.3 years ago by Anton Nekrutenko1.7k

Latest awards to Anton Nekrutenko

Appreciated 14 months ago, created a post with more than 5 votes. For A: TopHat tool missing?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: TopHat tool missing?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Creating a Workflow for Variant Detection for 200 samples
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Creating a Workflow for Variant Detection for 200 samples
Centurion 5.4 years ago, created 100 posts.

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