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Comment: Comment: How do I find allele frequencies from GATK output?
14 months ago by mgranada3 ▴ 60
0
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1
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2.2k
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Comment: Comment: How do I find allele frequencies from GATK output?
14 months ago by mgranada3 ▴ 60
3
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1
reply
855
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Why does the AD value of my VCF file display 3 values?
GATK vcf SnpEff
updated 14 months ago by 23k • written 14 months ago by ▴ 60
0
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0
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844
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Comment: Comment: Where do I gather indel and frameshift information in SnpEff output?
14 months ago by mgranada3 ▴ 60
0
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2
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1.0k
views
Why does 1 variant produce 3 genes as a result?
GATK SnpEff
updated 14 months ago by 89k • written 15 months ago by ▴ 60
0
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2
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844
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Where do I gather indel and frameshift information in SnpEff output?
frameshift WGWPS SnpEff GATK indels
14 months ago by mgranada3 ▴ 60
0
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1
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1.2k
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Comment: Comment: What's next after GATK variant calling pipeline?
15 months ago by mgranada3 ▴ 60
0
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1
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2.2k
views
Comment: Comment: How do I find allele frequencies from GATK output?
15 months ago by mgranada3 ▴ 60
5
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9
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2.2k
views
How do I find allele frequencies from GATK output?
allele-frequency GATK muller-plot
updated 14 months ago by ▴ 350 • written 15 months ago by ▴ 60
0
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0
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2.2k
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Comment: Comment: How do I find allele frequencies from GATK output?
15 months ago by mgranada3 ▴ 60
1
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3
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1.2k
views
What's next after GATK variant calling pipeline?
GATK pipeline figures DNA-seq
updated 15 months ago by 56k • written 18 months ago by ▴ 60
0
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1
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653
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK recalibration
updated 18 months ago by 154k • written 18 months ago by ▴ 60
0
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0
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1.5k
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Comment: Comment: Sorted bam files have zero content
22 months ago by mgranada3 ▴ 60
0
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0
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1.5k
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Comment: Comment: Sorted bam files have zero content
22 months ago by mgranada3 ▴ 60
2
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4
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1.5k
views
Sorted bam files have zero content
bam picard DNA-seq sorted
updated 22 months ago by 56k • written 22 months ago by ▴ 60
0
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1
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983
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Comment: Comment: Does samtools output a new .bam file after I add a read group to it?
22 months ago by mgranada3 ▴ 60
1
vote
3
replies
983
views
Does samtools output a new .bam file after I add a read group to it?
samtools readgroup gatk
updated 22 months ago by 166k • written 22 months ago by ▴ 60
0
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0
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1.5k
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Comment: Comment: Bwa-mem2 indexing not working down stream
23 months ago by mgranada3 ▴ 60
0
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2
replies
1.5k
views
Bwa-mem2 indexing not working down stream
bwa-mem2 index fasta
23 months ago by mgranada3 ▴ 60
0
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1
reply
875
views
Sorted bam files are empty after sorting them from bam
bam dna
updated 23 months ago by 45k • written 23 months ago by ▴ 60
0
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0
replies
775
views
Survival analysis in R keeps censoring figure with no censored data.
R survival-analysis censor
updated 2.0 years ago by 45k • written 2.0 years ago by ▴ 60
1
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2
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2.8k
views
What is an appropriate cut off for p-values and log fold changes during the analysis of a time course global gene expression experiment using DESeq2?
LFC Deseq2 p-value
updated 2.2 years ago by ▴ 380 • written 2.2 years ago by ▴ 60
1
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2
replies
2.5k
views
How to choose BWA-MEM2 settings
BWA-MEM2 DNA-seq bash
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 60
0
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1
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1.8k
views
Comment: Comment: How do I add row names to pheatmap() when I am using a pre-normalized matrix?
2.5 years ago by mgranada3 ▴ 60
0
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1
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1.8k
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Comment: Comment: How do I add row names to pheatmap() when I am using a pre-normalized matrix?
2.5 years ago by mgranada3 ▴ 60
0
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4
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1.8k
views
How do I add row names to pheatmap() when I am using a pre-normalized matrix?
pheatmap heatmap rna-seq
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by ▴ 60
2
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5
replies
4.0k
views
6 follow
How can I make all my PCA plots the same shape using ggplots?
deseq2 axis ggplots
updated 2.6 years ago by ▴ 40 • written 2.6 years ago by ▴ 60
0
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0
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5.9k
views
Comment: Comment: In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC
2.6 years ago by mgranada3 ▴ 60
0
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1
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5.9k
views
Comment: Comment: In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC
2.6 years ago by mgranada3 ▴ 60
6
votes
4
replies
5.9k
views
In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC2?
pc1 deseq2 plotpca pc2
2.6 years ago by mgranada3 ▴ 60
2
votes
2
replies
1.7k
views
How do I extract gene names from different portions of my heatmap?
pheatmap heatmap deseq2
updated 3.2 years ago by 9.0k • written 3.2 years ago by ▴ 60
0
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0
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10k
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Comment: Comment: How to export rld (rlog) or vsd values from DESeq2?
3.2 years ago by mgranada3 ▴ 60
0
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0
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3.4k
views
Comment: Comment: StringTie FPKM output to DESeq2 input
3.2 years ago by mgranada3 ▴ 60
0
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1
reply
1.8k
views
Comment: Comment: What are the values shown on DESEQ2 heatmap legend?
3.2 years ago by mgranada3 ▴ 60
0
votes
3
replies
1.8k
views
What are the values shown on DESEQ2 heatmap legend?
heatmap RNA-seq deseq2 R pheatmap
updated 3.2 years ago by 4.1k • written 3.2 years ago by ▴ 60
0
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1
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3.3k
views
Comment: Comment: How do you normalize a heat map to the control?
3.3 years ago by mgranada3 ▴ 60
2
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3
replies
3.3k
views
How do you normalize a heat map to the control?
heatmap RNA-seq DESeq2 R pheatmap
3.2 years ago by mgranada3 ▴ 60
3
votes
3
replies
1.4k
views
When looking at a heatmap created by DESeq2, how can I find what genes are in specific regions of interest?
pheatmap deseq2 heatmap rnaseq R
updated 3.6 years ago by 90k • written 3.6 years ago by ▴ 60
0
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1
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3.4k
views
Comment: Comment: When making a heat map with normalized data, should you still see the control da
3.7 years ago by mgranada3 ▴ 60
0
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3
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3.4k
views
When making a heat map with normalized data, should you still see the control data?
RNA-seq pheat R
updated 3.7 years ago by ▴ 220 • written 3.7 years ago by ▴ 60
0
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0
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1.7k
views
Comment: Comment: featureCounts output has letters and +/- sign
3.9 years ago by mgranada3 ▴ 60
0
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4
replies
1.7k
views
featureCounts output has letters and +/- sign
rnaseq featurecounts deseq2
3.9 years ago by mgranada3 ▴ 60
0
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1
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1.7k
views
Comment: Comment: featureCounts output has letters and +/- sign
3.9 years ago by mgranada3 ▴ 60
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