Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
0
votes
1
reply
1.1k
views
Comment: Comment: How do I find allele frequencies from GATK output?
4 months ago by mgranada3 ▴ 50
0
votes
1
reply
1.1k
views
Comment: Comment: How do I find allele frequencies from GATK output?
4 months ago by mgranada3 ▴ 50
3
votes
1
reply
369
views
Why does the AD value of my VCF file display 3 values?
GATK vcf SnpEff
updated 4 months ago by 23k • written 4 months ago by ▴ 50
0
votes
0
replies
379
views
Comment: Comment: Where do I gather indel and frameshift information in SnpEff output?
5 months ago by mgranada3 ▴ 50
0
votes
2
replies
483
views
Why does 1 variant produce 3 genes as a result?
GATK SnpEff
updated 5 months ago by 88k • written 5 months ago by ▴ 50
0
votes
2
replies
379
views
Where do I gather indel and frameshift information in SnpEff output?
frameshift WGWPS SnpEff GATK indels
5 months ago by mgranada3 ▴ 50
0
votes
1
reply
632
views
Comment: Comment: What's next after GATK variant calling pipeline?
5 months ago by mgranada3 ▴ 50
0
votes
1
reply
1.1k
views
Comment: Comment: How do I find allele frequencies from GATK output?
5 months ago by mgranada3 ▴ 50
5
votes
9
replies
1.1k
views
How do I find allele frequencies from GATK output?
allele-frequency GATK muller-plot
updated 4 months ago by ▴ 350 • written 6 months ago by ▴ 50
0
votes
0
replies
1.1k
views
Comment: Comment: How do I find allele frequencies from GATK output?
5 months ago by mgranada3 ▴ 50
1
vote
3
replies
632
views
What's next after GATK variant calling pipeline?
GATK pipeline figures DNA-seq
updated 5 months ago by 55k • written 8 months ago by ▴ 50
0
votes
1
reply
419
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK recalibration
updated 9 months ago by 149k • written 9 months ago by ▴ 50
0
votes
0
replies
843
views
Comment: Comment: Sorted bam files have zero content
12 months ago by mgranada3 ▴ 50
0
votes
0
replies
843
views
Comment: Comment: Sorted bam files have zero content
12 months ago by mgranada3 ▴ 50
2
votes
4
replies
843
views
Sorted bam files have zero content
bam picard DNA-seq sorted
updated 12 months ago by 55k • written 12 months ago by ▴ 50
0
votes
1
reply
654
views
Comment: Comment: Does samtools output a new .bam file after I add a read group to it?
13 months ago by mgranada3 ▴ 50
1
vote
3
replies
654
views
Does samtools output a new .bam file after I add a read group to it?
samtools readgroup gatk
updated 13 months ago by 165k • written 13 months ago by ▴ 50
0
votes
0
replies
1.0k
views
Comment: Comment: Bwa-mem2 indexing not working down stream
13 months ago by mgranada3 ▴ 50
0
votes
2
replies
1.0k
views
Bwa-mem2 indexing not working down stream
bwa-mem2 index fasta
13 months ago by mgranada3 ▴ 50
0
votes
1
reply
577
views
Sorted bam files are empty after sorting them from bam
bam dna
updated 14 months ago by 44k • written 14 months ago by ▴ 50
0
votes
0
replies
536
views
Survival analysis in R keeps censoring figure with no censored data.
R survival-analysis censor
updated 15 months ago by 44k • written 15 months ago by ▴ 50
1
vote
2
replies
1.9k
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 17 months ago by ▴ 280 • written 17 months ago by ▴ 50
1
vote
2
replies
1.5k
views
How to choose BWA-MEM2 settings
BWA-MEM2 DNA-seq bash
updated 18 months ago by 44k • written 18 months ago by ▴ 50
0
votes
1
reply
1.3k
views
Comment: Comment: How do I add row names to pheatmap() when I am using a pre-normalized matrix?
20 months ago by mgranada3 ▴ 50
0
votes
1
reply
1.3k
views
Comment: Comment: How do I add row names to pheatmap() when I am using a pre-normalized matrix?
20 months ago by mgranada3 ▴ 50
0
votes
4
replies
1.3k
views
How do I add row names to pheatmap() when I am using a pre-normalized matrix?
pheatmap heatmap rna-seq
updated 20 months ago by ★ 1.8k • written 20 months ago by ▴ 50
1
vote
5
replies
2.7k
views
6 follow
How can I make all my PCA plots the same shape using ggplots?
deseq2 axis ggplots
updated 21 months ago by ▴ 20 • written 21 months ago by ▴ 50
0
votes
0
replies
4.0k
views
Comment: Comment: In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC
21 months ago by mgranada3 ▴ 50
0
votes
1
reply
4.0k
views
Comment: Comment: In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC
21 months ago by mgranada3 ▴ 50
6
votes
4
replies
4.0k
views
In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC2?
pc1 deseq2 plotpca pc2
21 months ago by mgranada3 ▴ 50
2
votes
2
replies
1.1k
views
How do I extract gene names from different portions of my heatmap?
pheatmap heatmap deseq2
updated 2.4 years ago by 9.0k • written 2.4 years ago by ▴ 50
0
votes
0
replies
9.1k
views
Comment: Comment: How to export rld (rlog) or vsd values from DESeq2?
2.4 years ago by mgranada3 ▴ 50
0
votes
0
replies
2.8k
views
Comment: Comment: StringTie FPKM output to DESeq2 input
2.4 years ago by mgranada3 ▴ 50
0
votes
1
reply
1.3k
views
Comment: Comment: What are the values shown on DESEQ2 heatmap legend?
2.4 years ago by mgranada3 ▴ 50
0
votes
3
replies
1.3k
views
What are the values shown on DESEQ2 heatmap legend?
heatmap RNA-seq deseq2 R pheatmap
updated 2.4 years ago by 4.1k • written 2.4 years ago by ▴ 50
0
votes
1
reply
2.3k
views
Comment: Comment: How do you normalize a heat map to the control?
2.5 years ago by mgranada3 ▴ 50
2
votes
3
replies
2.3k
views
How do you normalize a heat map to the control?
heatmap RNA-seq DESeq2 R pheatmap
2.4 years ago by mgranada3 ▴ 50
3
votes
3
replies
1.1k
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 2.8 years ago by 86k • written 2.8 years ago by ▴ 50
0
votes
1
reply
2.8k
views
Comment: Comment: When making a heat map with normalized data, should you still see the control da
2.9 years ago by mgranada3 ▴ 50
0
votes
3
replies
2.8k
views
When making a heat map with normalized data, should you still see the control data?
RNA-seq pheat R
updated 2.9 years ago by ▴ 220 • written 2.9 years ago by ▴ 50
0
votes
0
replies
1.3k
views
Comment: Comment: featureCounts output has letters and +/- sign
3.1 years ago by mgranada3 ▴ 50
0
votes
4
replies
1.3k
views
featureCounts output has letters and +/- sign
rnaseq featurecounts deseq2
3.1 years ago by mgranada3 ▴ 50
0
votes
1
reply
1.3k
views
Comment: Comment: featureCounts output has letters and +/- sign
3.1 years ago by mgranada3 ▴ 50
43 results • Page 1 of 1
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6