User: rodd

gravatar for rodd
rodd100
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100
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Trusted
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London, United Kingdom
Twitter:
@3RDuarte
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1 day, 8 hours ago
Joined:
5 years, 4 months ago
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Posts by rodd

<prev • 44 results • page 1 of 5 • next >
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Answer: A: Testing similarity between functional genomic annotations
... I am calculating the similarity between long binary vectors (80 million in length) in R by importing my annotations as matrices (with each column corresponding to an annotation, and each row corresponding to the base pair position in the genome [0/1 if the SNP belongs to an annotation or not]). I am ...
written 5 months ago by rodd100
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Testing similarity between functional genomic annotations
... Hi folks! I have 1000+ binary vectors of the same length that consist of 0/1 positions corresponding to variants in the human genome and their functional annotation (i.e. transcription factor binding sites, protein-coding regions, methylation sites, etc.). Thus, each vector differs in the order, fr ...
functional genomics garfield genomic annotations R written 7 months ago by rodd100
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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 7 months ago by rodd100
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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 7 months ago by rodd100
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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 7 months ago by rodd100
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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 7 months ago by rodd100
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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 7 months ago by rodd100
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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 7 months ago by rodd100
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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 7 months ago by rodd100
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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 7 months ago by rodd100

Latest awards to rodd

Voter 7 months ago, voted more than 100 times.
Student 8 months ago, asked a question with at least 3 up-votes. For Effect of gene size on WGCNA
Supporter 20 months ago, voted at least 25 times.
Epic Question 3.1 years ago, created a question with more than 10,000 views. For trimming fastq files with Trimmomatic
Great Question 3.3 years ago, created a question with more than 5,000 views. For trimming fastq files with Trimmomatic
Popular Question 4.8 years ago, created a question with more than 1,000 views. For trimming fastq files with Trimmomatic

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