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2
votes
4
replies
417
views
Sorted bam files have zero content
bam picard DNA-seq sorted
updated 3 months ago by 54k • written 3 months ago by ▴ 30
1
vote
3
replies
390
views
Does samtools output a new .bam file after I add a read group to it?
samtools readgroup gatk
updated 3 months ago by 161k • written 3 months ago by ▴ 30
0
votes
2
replies
541
views
Bwa-mem2 indexing not working down stream
bwa-mem2 index fasta
4 months ago by mgranada3 ▴ 30
0
votes
1
reply
343
views
Sorted bam files are empty after sorting them from bam
bam dna
updated 4 months ago by 43k • written 4 months ago by ▴ 30
0
votes
0
replies
376
views
Survival analysis in R keeps censoring figure with no censored data.
R survival-analysis censor
updated 5 months ago by 43k • written 5 months ago by ▴ 30
1
vote
2
replies
1.2k
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 7 months ago by ▴ 190 • written 8 months ago by ▴ 30
1
vote
2
replies
987
views
How to choose BWA-MEM2 settings
BWA-MEM2 DNA-seq bash
updated 9 months ago by 43k • written 9 months ago by ▴ 30
0
votes
4
replies
861
views
How do I add row names to pheatmap() when I am using a pre-normalized matrix?
pheatmap heatmap rna-seq
updated 11 months ago by ★ 1.7k • written 11 months ago by ▴ 30
1
vote
5
replies
1.6k
views
6 follow
How can I make all my PCA plots the same shape using ggplots?
deseq2 axis ggplots
updated 12 months ago by ▴ 10 • written 12 months ago by ▴ 30
6
votes
4
replies
2.4k
views
In DESeq2, using plotPCA how do I go about extracting genes making up PC1 and PC2?
pc1 deseq2 plotpca pc2
12 months ago by mgranada3 ▴ 30
2
votes
2
replies
778
views
How do I extract gene names from different portions of my heatmap?
pheatmap heatmap deseq2
updated 19 months ago by 8.9k • written 19 months ago by ▴ 30
0
votes
3
replies
1.0k
views
What are the values shown on DESEQ2 heatmap legend?
heatmap RNA-seq deseq2 R pheatmap
updated 20 months ago by 4.1k • written 20 months ago by ▴ 30
1
vote
3
replies
1.6k
views
How do you normalize a heat map to the control?
heatmap RNA-seq DESeq2 R pheatmap
20 months ago by mgranada3 ▴ 30
3
votes
3
replies
862
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 2.1 years ago by 81k • written 2.1 years ago by ▴ 30
0
votes
3
replies
2.2k
views
When making a heat map with normalized data, should you still see the control data?
RNA-seq pheat R
updated 2.2 years ago by ▴ 140 • written 2.2 years ago by ▴ 30
0
votes
4
replies
1.1k
views
featureCounts output has letters and +/- sign
rnaseq featurecounts deseq2
2.3 years ago by mgranada3 ▴ 30
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