User: caggtaagtat

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caggtaagtat1.3k
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Posts by caggtaagtat

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Comment: C: Doubt on removing duplicates on amplicon sequencing data
... Would you have to remove duplicates, when comparing abundance of two transcript isoforms of a gene? ...
written 4 days ago by caggtaagtat1.3k
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Comment: C: Over-Expressed Gene Sample
... Your welcome, I think, the effect on the rest of the genes will be very low though, if you don't include the expression vector in the reference genome during alignment. ...
written 5 days ago by caggtaagtat1.3k
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Answer: A: Over-Expressed Gene Sample
... Hi, if this overexpression was induced by transfecting or transduction of cells with an expression vector, you should add the sequence of the resulting transcript in your reference genome during alignment of the reads. The reason for this is that sometimes, expression vectors use different UTRs tha ...
written 6 days ago by caggtaagtat1.3k
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Comment: C: Does PCA results impact on DESeq2 design choices?
... Your welcome, always happy to discuss :) 1) From this plot, I personally would think, that PC1 is indeed batch related, because positives from batch pink are far right and positives from batch blue seem to concentrate to the left (on a PC1 axis that describes 37% of the variance which is not low). ...
written 12 days ago by caggtaagtat1.3k
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Comment: C: Tool for calculation of free energy of most likely secondary structure of an RNA
... Ok, so there is an R-package called LncFinder which can be used to apply ViennaRNA in R, in case someone is interested. ...
written 13 days ago by caggtaagtat1.3k
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Comment: C: Tool for calculation of free energy of most likely secondary structure of an RNA
... thank you very much! I did no see that after my initial quick readthrough and will definitly look into it. ...
written 13 days ago by caggtaagtat1.3k
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Tool for calculation of free energy of most likely secondary structure of an RNA sequence
... Hi, I'm looking for an tool, which can calculate the free energy of the most likely secondary structure of an short RNA sequence (50-100nt), for the developement of an R-package. The famous mfold tool unfortunately seems to complex to integrate it into an package (the authors are contacted). I want ...
rna structure free energy written 13 days ago by caggtaagtat1.3k
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Answer: A: Does PCA results impact on DESeq2 design choices?
... Hi, looking at the description of the data on GEO, it mentions that they also saw differences in gene expression depending on age and sex of the individuals, as well as infection time course (they say they included it as interaction terms). It makes sense that gene expression could vary between an ...
written 13 days ago by caggtaagtat1.3k
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Comment: C: How to obtain list of reference genes for RNA-seq analysis
... Ensembl is currently under maintenance. You need it to add the gene names to the results file, since the salmon output only had the ensembl ids? ...
written 14 days ago by caggtaagtat1.3k
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Answer: A: Mann-Whitney Test/Wilcoxon but for individual genes between case and control
... Could it be, that the authors just performed a Mann-Whitney test on the normalized expression values per gene? Its basically similar to a t-test, where you have two population of values. In this case one population would be the normalized expression values of the 20 control cases and the second popu ...
written 14 days ago by caggtaagtat1.3k

Latest awards to caggtaagtat

Scholar 4 weeks ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 7 weeks ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: How to create custom gtf annotation file?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Scholar 3 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Guru 4 months ago, received more than 100 upvotes.
Appreciated 4 months ago, created a post with more than 5 votes. For A: Question about exon/intron counting in RNA-seq dataset analysis
Popular Question 5 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Popular Question 6 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Popular Question 7 months ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Popular Question 8 months ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Popular Question 9 months ago, created a question with more than 1,000 views. For Genebank to GTF recommended tool?
Scholar 10 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 11 months ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Scholar 11 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 13 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: How to create custom gtf annotation file?
Popular Question 14 months ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Question about exon/intron counting in RNA-seq dataset analysis

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