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Comment: Comment: How do I find allele frequencies from GATK output?
19 days ago by mgranada3 ▴ 50
0
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1
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744
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Comment: Comment: How do I find allele frequencies from GATK output?
4 weeks ago by mgranada3 ▴ 50
3
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1
reply
256
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Why does the AD value of my VCF file display 3 values?
GATK vcf SnpEff
updated 4 weeks ago by 22k • written 4 weeks ago by ▴ 50
0
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0
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268
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Comment: Comment: Where do I gather indel and frameshift information in SnpEff output?
5 weeks ago by mgranada3 ▴ 50
0
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2
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357
views
Why does 1 variant produce 3 genes as a result?
GATK SnpEff
updated 5 weeks ago by 88k • written 8 weeks ago by ▴ 50
0
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2
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268
views
Where do I gather indel and frameshift information in SnpEff output?
frameshift WGWPS SnpEff GATK indels
5 weeks ago by mgranada3 ▴ 50
0
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1
reply
417
views
Comment: Comment: What's next after GATK variant calling pipeline?
8 weeks ago by mgranada3 ▴ 50
0
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1
reply
744
views
Comment: Comment: How do I find allele frequencies from GATK output?
8 weeks ago by mgranada3 ▴ 50
5
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9
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744
views
How do I find allele frequencies from GATK output?
allele-frequency GATK muller-plot
updated 19 days ago by ▴ 350 • written 9 weeks ago by ▴ 50
0
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0
replies
744
views
Comment: Comment: How do I find allele frequencies from GATK output?
9 weeks ago by mgranada3 ▴ 50
1
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3
replies
417
views
What's next after GATK variant calling pipeline?
GATK pipeline figures DNA-seq
updated 8 weeks ago by 55k • written 4 months ago by ▴ 50
0
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1
reply
335
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK recalibration
updated 5 months ago by 146k • written 5 months ago by ▴ 50
0
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0
replies
692
views
Comment: Comment: Sorted bam files have zero content
8 months ago by mgranada3 ▴ 50
0
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0
replies
692
views
Comment: Comment: Sorted bam files have zero content
8 months ago by mgranada3 ▴ 50
2
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4
replies
692
views
Sorted bam files have zero content
bam picard DNA-seq sorted
updated 8 months ago by 55k • written 9 months ago by ▴ 50
0
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1
reply
562
views
Comment: Comment: Does samtools output a new .bam file after I add a read group to it?
9 months ago by mgranada3 ▴ 50
1
vote
3
replies
562
views
Does samtools output a new .bam file after I add a read group to it?
samtools readgroup gatk
updated 9 months ago by 164k • written 9 months ago by ▴ 50
0
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0
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815
views
Comment: Comment: Bwa-mem2 indexing not working down stream
9 months ago by mgranada3 ▴ 50
0
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2
replies
815
views
Bwa-mem2 indexing not working down stream
bwa-mem2 index fasta
9 months ago by mgranada3 ▴ 50
0
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1
reply
496
views
Sorted bam files are empty after sorting them from bam
bam dna
updated 10 months ago by 44k • written 10 months ago by ▴ 50
0
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0
replies
471
views
Survival analysis in R keeps censoring figure with no censored data.
R survival-analysis censor
updated 11 months ago by 44k • written 11 months ago by ▴ 50
1
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2
replies
1.6k
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 13 months ago by ▴ 270 • written 13 months ago by ▴ 50
1
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2
replies
1.3k
views
How to choose BWA-MEM2 settings
BWA-MEM2 DNA-seq bash
updated 14 months ago by 44k • written 14 months ago by ▴ 50
0
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1
reply
1.1k
views
Comment: Comment: How do I add row names to pheatmap() when I am using a pre-normalized matrix?
16 months ago by mgranada3 ▴ 50
0
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1
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1.1k
views
Comment: Comment: How do I add row names to pheatmap() when I am using a pre-normalized matrix?
16 months ago by mgranada3 ▴ 50
0
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4
replies
1.1k
views
How do I add row names to pheatmap() when I am using a pre-normalized matrix?
pheatmap heatmap rna-seq
updated 16 months ago by ★ 1.8k • written 16 months ago by ▴ 50
1
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5
replies
2.2k
views
6 follow
How can I make all my PCA plots the same shape using ggplots?
deseq2 axis ggplots
updated 17 months ago by ▴ 20 • written 17 months ago by ▴ 50
0
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0
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3.4k
views
Comment: Comment: In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC
18 months ago by mgranada3 ▴ 50
0
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1
reply
3.4k
views
Comment: Comment: In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC
18 months ago by mgranada3 ▴ 50
6
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4
replies
3.4k
views
In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC2?
pc1 deseq2 plotpca pc2
18 months ago by mgranada3 ▴ 50
2
votes
2
replies
952
views
How do I extract gene names from different portions of my heatmap?
pheatmap heatmap deseq2
updated 2.1 years ago by 9.0k • written 2.1 years ago by ▴ 50
0
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0
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8.8k
views
Comment: Comment: How to export rld (rlog) or vsd values from DESeq2?
2.1 years ago by mgranada3 ▴ 50
0
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0
replies
2.6k
views
Comment: Comment: StringTie FPKM output to DESeq2 input
2.1 years ago by mgranada3 ▴ 50
0
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1
reply
1.2k
views
Comment: Comment: What are the values shown on DESEQ2 heatmap legend?
2.1 years ago by mgranada3 ▴ 50
0
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3
replies
1.2k
views
What are the values shown on DESEQ2 heatmap legend?
heatmap RNA-seq deseq2 R pheatmap
updated 2.1 years ago by 4.1k • written 2.1 years ago by ▴ 50
0
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1
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2.0k
views
Comment: Comment: How do you normalize a heat map to the control?
2.2 years ago by mgranada3 ▴ 50
2
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3
replies
2.0k
views
How do you normalize a heat map to the control?
heatmap RNA-seq DESeq2 R pheatmap
2.1 years ago by mgranada3 ▴ 50
3
votes
3
replies
1.0k
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 2.5 years ago by 84k • written 2.5 years ago by ▴ 50
0
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1
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2.5k
views
Comment: Comment: When making a heat map with normalized data, should you still see the control da
2.6 years ago by mgranada3 ▴ 50
0
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3
replies
2.5k
views
When making a heat map with normalized data, should you still see the control data?
RNA-seq pheat R
updated 2.6 years ago by ▴ 190 • written 2.6 years ago by ▴ 50
0
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0
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1.2k
views
Comment: Comment: featureCounts output has letters and +/- sign
2.8 years ago by mgranada3 ▴ 50
0
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4
replies
1.2k
views
featureCounts output has letters and +/- sign
rnaseq featurecounts deseq2
2.8 years ago by mgranada3 ▴ 50
0
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1
reply
1.2k
views
Comment: Comment: featureCounts output has letters and +/- sign
2.8 years ago by mgranada3 ▴ 50
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