User: theobroma22

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theobroma22980
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Posts by theobroma22

<prev • 261 results • page 1 of 27 • next >
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Comment: C: Query regarding KEGG database
... So, you have genes that have multiple KO numbers or are in multiple pathways? ...
written 4 days ago by theobroma22980
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Answer: A: GC content biases in RNA-seq data of A.thaliana
... If you did it correctly you have to consider that 36 percent and 52 percent are percentages, or ratios. Your transcriptome is certainly smaller than the genome, and as you said your transcriptome has a higher GC content. So, it's quite plausible there's nothing wrong. ...
written 5 days ago by theobroma22980
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Comment: C: expression Quantitative trait loci
... It may be better for you to contact a lab of your interest? ...
written 5 days ago by theobroma22980
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Comment: C: expression Quantitative trait loci
... Water on a burning topic. ...
written 5 days ago by theobroma22980
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Comment: C: Confirming predicted gene model by RNA-Seq data
... Can you upvote or confirm that either of these processes worked for you please. ...
written 5 days ago by theobroma22980
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Comment: C: kal's test on rpkm vs raw counts
... Not at all. You have to consider the experimental design of SAGE vs. RNA-seq, which is what you used. ...
written 5 days ago by theobroma22980
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Answer: A: kal's test on rpkm vs raw counts
... CLC Bio is a licensed platform, so it may be best for you to contact CLC to get an answer to your question. However, Karl's test is for the count data and not RPKM. ...
written 6 days ago by theobroma22980
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Answer: A: Compare RNAseq Data from two independent runs?
... You may have batch effects if the multiplexing for the lane was different between runs. You can try processing your data thru the SVA package available on Bioconductor. ...
written 10 days ago by theobroma22980
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Answer: A: Gene Expression Downstream Analysis
... Since you are working with human tissues, you have the EntrezIDs. Check out the SPIA package available on the Bioconductor website. ...
written 10 days ago by theobroma22980
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Comment: C: range of fold change in RNA seq
... Thousands can be acceptable. Tens of thousands is usually scrutinized. ...
written 10 days ago by theobroma22980

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Scholar 14 days ago, created an answer that has been accepted. For A: Creating a targets matrix
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