User: Ram

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Ram110
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Bioinformatician

Posts by Ram

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Comment: C: DESeq2 followed by GSEA
... Below mentioned is the description from DESeq2 Vignette for p-values in case for p-adj : By default, independent filtering is performed to select a set of genes for multiple test correction which will optimize the number of adjusted p-values less than a given critical value ‘alpha’ ( ...
written 8 months ago by Ram110
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Answer: A: DESeq2 followed by GSEA
... I think there are two ways of generating the GSEA preranked list: 1) by log2FC; 2) by p value. You might take a look at this previous thread: [Gene Set Enrichment Analysis after DESeq2][1] [1]: http://www.biostars.org/p/279097/ ...
written 8 months ago by Ram110
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Comment: C: Can't fetch pathways by entrez id?
... You can use like this : Example : x <- c(1,2,3,4,NA,5) na.omit(x) x >1 2 3 4 5 ...
written 8 months ago by Ram110
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Answer: A: High Throughput Screening for ligands in case of known protein-protein binding c
... I think these threads may be helpful for you : [Ligand Docking In The Minimized Protein.][1] [Protein Protein Docking][2] [1]: http://www.biostars.org/p/12574/ [2]: http://www.biostars.org/p/48596/ ...
written 8 months ago by Ram110
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Answer: A: finding mutation from RNA seq data
... You can find this paper helpful describing SNPiR pipeline : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676881/ ...
written 8 months ago by Ram110
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Answer: A: Visualization software for large variations
... Yes, you can use junction files obtained along with alignment files by using available alignment tool. After that you can import junction files for obtaining Circos plot by using Circos software: http://circos.ca/software/ ...
written 8 months ago by Ram110
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Answer: A: Generating a Circos Plot
... For generating a Circos plot you can use online Circos software : http://circos.ca/software/ If you are comfortable using R, you can implement RCircos Package in R. ...
written 8 months ago by Ram110
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Answer: A: problem in fastq-dump of SRA file
... I think you should use the correct path for the command like this: /path/fastq-dump --split-3 file.sra ...
written 8 months ago by Ram110
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Answer: A: RNA seq data for prediction of novel proteins
... So for your first step for prediction of RNA editing sites, you can use below mentioned pipeline : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676881/ Similarly to obtain Structure of protein you can use Protein Data Bank (PDB). ...
written 8 months ago by Ram110
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Answer: C: How to Visulaise Genes per sample (Text visualisation)
... Hi, I think circos.track from circlize package will be quite useful for your request : https://www.rdocumentation.org/packages/dendextend/versions/1.6.0/topics/circlize_dendrogram ...
written 8 months ago by Ram110

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