User: rodd

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rodd80
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London, United Kingdom
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Posts by rodd

<prev • 42 results • page 1 of 5 • next >
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Comment: C: How to interpret Per sequence GC content module in FastQC for RNA-seq data?
... Hi genomax, thanks once again for your input! No, this is RNA-seq data from Poly-A enriched total RNA extracted from a human cell line (NEBNext Ultra Directional RNA Library Prep Kit for Illumina), so I am a bit surprised with the high GC peak I see in every sample. The technicians who constructed t ...
written 2 days ago by rodd80
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Comment: C: filtering rRNA from fastq files or mapping results
... Dear Devon, Karl et al. I came across an issue with rRNA contamination in my RNA-seq data (poly-A sequencing), and I found several posts about this issue. I observed contradictory or not very straightforward answers regarding what I can do next. For example, here you're recommending to not remove r ...
written 2 days ago by rodd80
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Comment: C: Correlation of modules calculated in separate WGCNA runs
... Sorry, this was a stupid question - I can just try calculating a consensus network using the full female set, the full male set, and the subsetted male set (three sets in one go)... That just came to me as soon as I pressed enter on this question lol (But I will leave the question here, because I am ...
written 3 days ago by rodd80
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Comment: C: How to interpret Per sequence GC content module in FastQC for RNA-seq data?
... Thanks for your suggestions, genomax, they're super helpful! I used SortMeRNA to remove rRNA from the reads in one sample, but the GC content distribution seen in FASTQC is pretty identical to the one observed prior to removing the rRNA. I would like to try option b), but I don't understand 100% wha ...
written 3 days ago by rodd80
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Comment: C: How to interpret Per sequence GC content module in FastQC for RNA-seq data?
... Oh, 3 "overrepresented sequences" detected in FASTQC (blasting to the same ribosomal protein) each account for around 12% of the sequences in one of my samples... eeek Is this bad? All other samples look similar. ...
written 4 days ago by rodd80
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Comment: C: How to interpret Per sequence GC content module in FastQC for RNA-seq data?
... Thanks, genomax! How can I estimate this? My alignment rate is between 75-80% for all samples, and the GC content distribution (after adapter trimming or not) looks like [this][1] (multiqc summary of fastqc analysis of all samples). Overrepresented sequences blast to ribosomal genes. [1]: https: ...
written 4 days ago by rodd80
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Comment: C: How to interpret Per sequence GC content module in FastQC for RNA-seq data?
... I am curious to know if there's a method for understanding if rRNA contamination (or other sources that could drive a shift in the GC content distribution) has an effect on differential gene expression. I am also analyzing samples with abnormal GC distribution (for which overrepresented sequences in ...
written 4 days ago by rodd80
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Comment: C: WGCNA pearson or bicor? Also, should I adjust module correlation Pvalues by Bonf
... oooooh, I just figured this out, I had to "force" the dimensions of the old table in the new table.. Sorry for the rookie's mistake lads. for (set in 1:nSets){ moduleTraitCor[[set]] = cor(consMEs[[set]]$data, Traits[[set]]$data, use = "p"); moduleTraitPvalue[[set]] = corPvalueFis ...
written 8 days ago by rodd80
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Comment: C: WGCNA pearson or bicor? Also, should I adjust module correlation Pvalues by Bonf
... Hi Kevin! I did initialize them (I updated the code above now to show that). When I View these variables after running the loop, they show a list of 2 (because I have two sets), but the 'dimensions' of each sub-list are different. The p.adjust function is merging all columns of moduleTraitPvalue ( ...
written 8 days ago by rodd80
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Comment: C: WGCNA pearson or bicor? Also, should I adjust module correlation Pvalues by Bonf
... Hi folks, thanks for the discussion! Sorry for jumping in, but I wanted to ask (sorry for the super newbie question!).. How do I plot the corrected values? I added the following line to correct the correlation P values (from a multExpr object, from a consensus analysis): moduleTraitCor = list() ...
written 9 days ago by rodd80

Latest awards to rodd

Voter 4 days ago, voted more than 100 times.
Student 10 days ago, asked a question with at least 3 up-votes. For Effect of gene size on WGCNA
Supporter 12 months ago, voted at least 25 times.
Epic Question 2.5 years ago, created a question with more than 10,000 views. For trimming fastq files with Trimmomatic
Great Question 2.7 years ago, created a question with more than 5,000 views. For trimming fastq files with Trimmomatic
Popular Question 4.2 years ago, created a question with more than 1,000 views. For trimming fastq files with Trimmomatic

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