User: GreenDiamond

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GreenDiamond70
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Posts by GreenDiamond

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Metatranscriptomics in sterile rooms
... Thank you, WouterDeCoster. I realize I did not state that very clear, so I just updated it in bold to show that I am looking for bioinformatics approaches (I am also looking for library-prep elsewhere). Thank you. ...
written 4 weeks ago by GreenDiamond70
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Metatranscriptomics in sterile rooms
... I am trying to determine state-of-the-art methods to conducting metatranscriptomic RNA-seq analysis of microbial ecology in sterile environments (like industrial clean rooms). Given the harshness and lack of nutrients in sterile indoor clean environments, the amount of DNA and RNA that can be obtain ...
metatranscriptomics sterile written 4 weeks ago by GreenDiamond70
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Comment: C: RNA-sequencing dataset analyzed twice: good and poor estimate of false-positive
... Thank you very much for these links and words of advice! As I said in my original post: "I am hoping to examine visually what DEGs 'look like' when they come from an analysis that has a poor false-positive rate estimation versus a good false-positive rate estimation.". I should have added a sentenc ...
written 9 months ago by GreenDiamond70
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RNA-sequencing dataset analyzed twice: good and poor estimate of false-positive rates
... I am trying to find an example where an RNA-sequencing dataset was analyzed in one manner that lead to a **poor** false-positive rate estimation, and then analyzed in another manner that lead to a **good** false-positive rate estimation. Ideally, both analysis methods led to DEGs: Only in the first ...
false-positive rna-seq written 9 months ago by GreenDiamond70 • updated 9 months ago by vchris_ngs4.5k
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Comment: C: Determine gene function for soyBean transcript
... Thank you for your very helpful comment! ...
written 9 months ago by GreenDiamond70
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Answer: A: Determine gene function for soyBean transcript
... Thanks @lessismore. I am trying the site you recommended, but am still uncertain how to obtain tentative functions of these genes. I am sorry if it might be obvious! In the search bar at the type right, I selected "SoyCyc" in the left field and typed each of the five gene names I listed in my origin ...
written 9 months ago by GreenDiamond70
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Determine gene function for soyBean transcript
... I recently performed an RNA-sequencing analysis on soybean transcripts, and am interested in learning more about five transcripts of interest. In the transcript .fasta file, these transcript names are listed in the following format: Glyma.18G057100.Wm82.a2.v1 Glyma.18G092200.Wm82.a2.v1 Glyma.09G164 ...
function transcript rna-seq written 9 months ago by GreenDiamond70 • updated 9 months ago by theobroma221.1k
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Example RNA-seq datasets that require specific normalizations
... Hello, I am wondering if there are any available example RNA-seq datasets that need to be normalized in specific ways (btwnLaneNormalization versus calcNormFactors)? If not, and more likely, are there any available methods to simulate RNA-seq datasets that could show why specific normalization (btw ...
normalization rna-seq written 10 months ago by GreenDiamond70
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Generating .xml file from list of genes using BLAST
... Hello, I need to generate an .xml file from BLAST starting with a list of genes (currently in .txt format). Do I require a script to do this, or is there an easier way to do this directly on the online BLAST website? Thank you...   ...
blast written 4.0 years ago by GreenDiamond70 • updated 4.0 years ago by Prakki Rama2.1k
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Answer: A: DAVID unable to determine the biological process/ function of gene list
... Thank you so much both for your answers! I am very thankful for it. I am working with Blast2Go right now. I have never used it before. But I am thinking I should follow protocol "Functional annotation in 3 steps: BLAST to find homologus sequences, MAPPING to retrieve GO terms and ANNOTATION to sele ...
written 4.0 years ago by GreenDiamond70

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Popular Question 9 months ago, created a question with more than 1,000 views. For Generating .xml file from list of genes using BLAST
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