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User: rmf

gravatar for rmf
rmf • 280
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280
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Posts by rmf

<prev • 99 results • page 1 of 10 • next >
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DESeq2 compare all levels
... For RNA-Seq DGE analysis using DESeq2, if I have a factor with let's say 5 levels: condition A A B B C C D D E E The standard workflow d <- DESeqDataSetFromMatrix(countData=counts,colData=meta,design=as.formula(~condition)) d <- DESeq2::es ...
deseq2 rna-seq differential gene expression written 16 days ago by rmf • 280 • updated 16 days ago by Kevin Blighe ♦ 24k
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Comment: C: RNA-Seq identify stably expressed genes
... It's not for normalisation. I actually want to find stably expressed genes. I want to find genes that do not change between tissues. One tissue is easy to get and other is hard. One of the questions is if the easy tissue can be use as a proxy for the hard-to-get tissue. ...
written 12 weeks ago by rmf • 280
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Comment: C: RNA-Seq identify stably expressed genes
... So, is it just a matter of running a standard DE analysis and then look for genes with low FC and high p-values? ...
written 12 weeks ago by rmf • 280
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Comment: C: RNA-Seq identify stably expressed genes
... Six replicates per tissue. ...
written 12 weeks ago by rmf • 280
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RNA-Seq identify stably expressed genes
... I normally use Limma for differential gene expression. This time, I am interested in significantly stably expressed genes rather than differentially expressed. So, I am looking for genes that change the least in expression. I am comparing two tissues. And the normal assumption of DGE 'most genes a ...
rna-seq dge written 12 weeks ago by rmf • 280
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Comment: C: bwa mem: Passing a variable to read group
... I have added an answer. ...
written 3 months ago by rmf • 280
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Answer: A: bwa mem: Passing a variable to read group
... What worked for me was to read the read group information from the fastq file during the mapping run. My read name in the fastq file looks like this: `@ST-E00274:188:H3JWNCCXY:4:1101:5142:1221 1:N:0:NTTGTA`. The bash file looks like this: #!/bin/bash header=$(zcat $1 | head -n 1) ...
written 3 months ago by rmf • 280
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GATK: .ped vs .fam and missing values
... In the GATK pipeline, it seems like I need to use a *.ped* file for `CalculateGenotypePosteriors` and a *.fam* file for `VariantsToBinaryPed`. What is the difference between *.ped* and *.fam* file? And how do I specify missing parents in both of them? Some options I've seen are zero (`0`), `NO_PAREN ...
variant-calling gatk snp written 3 months ago by rmf • 280 • updated 3 months ago by Kevin Blighe ♦ 24k
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Comment: C: RNASeq: Differential gene expression and qqplot
... Thanks for the input. The sample size is same as before: 24. ...
written 4 months ago by rmf • 280
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RNASeq: Differential gene expression and qqplot
... I ran DGE on my dataset using DESeq2 and Limma. I used the same dataset, similar settings and same GLM model (`~family+condition`). The number of DEGs I get are as below (based on unadjusted p-values <0.05 and BH adjusted q-values <0.05 shown separately): Tool num_degs_pval num_degs_qv ...
deseq2 rna-seq differential gene expression limma written 4 months ago by rmf • 280

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Popular Question 19 days ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
Popular Question 9 weeks ago, created a question with more than 1,000 views. For RNA-Seq experiment has low fold change
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Centurion 12 weeks ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
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Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 4 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 4 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Scholar 4 months ago, created an answer that has been accepted. For A: Regenotype vcf using some samples as reference
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Popular Question 10 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
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