User: GreenDiamond

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GreenDiamond70
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Posts by GreenDiamond

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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 10 days 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 19 days ago by GreenDiamond70 • updated 19 days ago by vchris_ngs4.0k
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Comment: C: Determine gene function for soyBean transcript
... Thank you for your very helpful comment! ...
written 19 days 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 20 days 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 21 days ago by GreenDiamond70 • updated 19 days ago by theobroma221.0k
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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 8 weeks 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 3.2 years ago by GreenDiamond70 • updated 3.2 years ago by Prakki Rama2.0k
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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 3.2 years ago by GreenDiamond70
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DAVID unable to determine the biological process/ function of gene list
... I have a list of DEGs from DESeq from A.digitifera coral. I put them into DAVID software as a list, selected Identifier as "OFFICIAL_GENE_SYMBOL", chose Gene List, and then submitted the list. Then, I chose "Option 1: Convert the gene list to DAVID". None of the genes were in the DAVID database, was ...
david biological process written 3.2 years ago by GreenDiamond70
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Translation Of Graph Theory Into Experimental Verification
... Hi BioStars, Graph theoretical approaches are becoming very common in bioinformatics. Have you ever come across a group that generated a network to construct hypotheses, and then used that information to design follow-up experiments that discovered something new and important? I am interested to s ...
translation graph written 3.6 years ago by GreenDiamond70 • updated 3.6 years ago by B. Arman Aksoy1.2k

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