User: Carlo Yague

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Carlo Yague2.0k
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Posts by Carlo Yague

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Comment: C: How to change depth of sequence in RNA-seq fastq files
... I think Charles clarified the issue in its last post. Indeed, downsampling in NGS is usually made at the read level, not the replicate level. Note that it can be faster and more efficient to downsample the **mapped** reads (.bam or .sam files) rather than the raw reads in order to avoid mapping mu ...
written 5 hours ago by Carlo Yague2.0k
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Comment: C: How to change depth of sequence in RNA-seq fastq files
... Replicates and depth are very different things so no, it's not ok to remove one replicate if you want to investigate the effect of depth of sequencing. [How do I down sample a fastq in Galaxy?][1] [1]: https://biostar.usegalaxy.org/p/10742/ ...
written 10 hours ago by Carlo Yague2.0k
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Comment: C: How many tests does it take to warrant a microarray/RNA-seq approach to differen
... Can we really use DESeq2 with continuous data (vs integer count) ? It's a genuine question, I really don't know. ...
written 8 days ago by Carlo Yague2.0k
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Comment: C: How to convincingly illustrate and discuss negative results in NGS.
... Yep, I thought the same thing ^^ More seriously, let's assume that we can't change the stringency because we want to keep the same parameters across the full study (that includes more conditions than X and Y). ...
written 17 days ago by Carlo Yague2.0k
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Comment: C: How to convincingly illustrate and discuss negative results in NGS.
... Thank you for your input. Yes, that could be an interesting point in some cases. However sometimes the genes are deregulated based on their "genomic features" (position on chromosomes, presence of introns, nearby ncRNAs, ...) rather than their biological function and there is no functional link (GO/ ...
written 18 days ago by Carlo Yague2.0k
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Forum: How to convincingly illustrate and discuss negative results in NGS.
... Hi everyone, In statistics and in science in general, it is always harder to convincingly show lack of effect rather than significant differences. In low throughput experiments, one can always report pvalues and show that the difference is not statistically significant but the situation is more com ...
forum negative results rna-seq deg written 18 days ago by Carlo Yague2.0k
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Comment: C: create plot from bed file
... what do you want to plot ? ...
written 19 days ago by Carlo Yague2.0k
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Comment: C: Simultaneously adding two different covariates in the model gives error in DESeq
... Can you elaborate ? In theory, a continuous covariate provides more information to the model than arbitrary categories so it should be better. Although it might not be the case if the relationship between the continuous covariate and gene expression is not linear... I'm not sure though. ...
written 19 days ago by Carlo Yague2.0k
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Comment: C: Simultaneously adding two different covariates in the model gives error in DESeq
... Yes, I think that it is a good idea to include the RIN score. ...
written 19 days ago by Carlo Yague2.0k
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Comment: C: Why genome seq A% ~= T% and G% ~= C%
... You are right, I forgot to reverse the fragments. Will edit later. EDITED. ...
written 20 days ago by Carlo Yague2.0k

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Commentator 10 hours ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 2 days ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 5 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 6 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 5 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
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