Moderator: swbarnes2

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Posts by swbarnes2

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Comment: C: General question about subsetting data for RNASeq DESe2 analysis
... Even doing PCA with all the genes, instead of the top 500 most variant ones, the batch effect is still 61%. But your think I gain more by keeping all, and putting "day" into the designs, instead of subsetting, and only comparing same-day samples? ...
written 2 days ago by swbarnes22.8k
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Comment: C: General question about subsetting data for RNASeq DESe2 analysis
... But my question is, is there anyway to know from the math alone if I'm better off splitting the samples, or keeping them together? Does it depend on whether or not it's expected to be biological versus batch effect? Or should I not worry about it the top 100 genes either way are mostly the same? ...
written 3 days ago by swbarnes22.8k
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Comment: C: General question about subsetting data for RNASeq DESe2 analysis
... The information I have on the experimental set-up and conditions is very limited. The first component, which splits the samples by the day of the Illumina run, accounts for 79% of the variance. But as far as I can tell, there were other conditions that differ between the samples run on the two da ...
written 3 days ago by swbarnes22.8k
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General question about subsetting data for RNASeq DESe2 analysis
... I have an experiment that is split into two halves. The experimental compound used is the same in each half, same type of sample, but the other conditions are different. When I do PCA, or look at the Euclidean distance between the samples, they definitely split into two halves. Would it be prefer ...
deseq2 rna-seq written 3 days ago by swbarnes22.8k
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Answer: A: Appropriate DESeq2 design for multi-factor comparison within group?
... You don't subset the file like that. You can use different settings in the results function to return the comparison you want. Make a new column in the phenoFile that concatenates the group and concentration, and then you can do "results(dds, contrast=c("new", "A10mL", "A150,L")) ...
written 9 days ago by swbarnes22.8k
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Comment: C: Understanding terms, specifically relating to GT:PL in a VCF file
... The sense and antisense strand are reverse complements of each other, they are essentially the same sequence. But a diploid organism has two copies of the whole genome, so each copy can have a different letter at a given point. A non-clonal mix of organisms can also show two (or more) different let ...
written 23 days ago by swbarnes22.8k
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Comment: C: How to convert BAM file from hg19 to hg38
... Many aligners will take .bam as input, so you don't have to convert to fastq prior to realigning. But yes, converting the SNP lists would probably be easiest. ...
written 5 weeks ago by swbarnes22.8k
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Comment: C: Remove mitochondrial reads from BAM files
... I'd count the lines, instead of looking at file sizes. ...
written 5 weeks ago by swbarnes22.8k
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Comment: C: Unsynchronized simultaneous reads on a single .bam file
... Consider using samtools mpileup on the whole chromosome, then use BEDTools intersect to get the overlap between your vcf and a bedfile of locations. ...
written 5 weeks ago by swbarnes22.8k
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Comment: C: DESeq2 multi-factor design
... Yeah, I guess you are right. Using Individual + Tissue was giving me the highest p-values,so I guess that's a sign that it was filtering away the most extraneous influences. Thanks. ...
written 6 weeks ago by swbarnes22.8k

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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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