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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 3 months ago by
swbarnes2
★ 1.3k • written 3 months ago by
Bo
• 0
0
votes
1
reply
531
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 14 months ago by
Michael Love
41k • written 14 months ago by
nico
• 0
0
votes
1
reply
1.8k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads
STAR
featureCounts
updated 16 months ago by
swbarnes2
★ 1.3k • written 16 months ago by
lalala
• 0
1
vote
3
replies
1.5k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
josephbrown
▴ 10
0
votes
1
reply
1.7k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
mohamedrefaat.1.1992
• 0
0
votes
1
reply
869
views
Using STAR and DESeq2 for circRNA analysis
STAR
deseq2
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
csijst
• 0
3
votes
2
replies
2.0k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq
featureCounts
STAR
minMQS
mapping quality score
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
Gary
▴ 20
0
votes
1
reply
884
views
weired output with featurecount
featurecounts
star
5.5 years ago
roghaiyeh.safari
• 0
0
votes
3
replies
3.2k
views
Handling pseudogenes in RNA-seq
rna-seq
pseudogenes
STAR
counts
updated 5.8 years ago by
Levi Waldron
★ 1.1k • written 5.8 years ago by
supremerulersuraj
• 0
0
votes
2
replies
2.9k
views
lncRNA annotation for featureCouns and STAR
lncRNA
featureCounts
STAR
annotation
updated 5.8 years ago by
Wei Shi
★ 3.6k • written 5.8 years ago by
inah
▴ 10
0
votes
2
replies
1.0k
views
BAM file into R from Illumina
bam file
STAR
Illumina
updated 5.9 years ago by
ta_awwad
▴ 10 • written 5.9 years ago by
soheilazareie
• 0
2
votes
2
replies
1.1k
views
Why does total unique map not equal to library size?
htseqcounts
star
rnaseq
6.6 years ago
Ahdee
▴ 50
2
votes
2
replies
7.2k
views
RNA STAR to DESeq2
deseq2
count matrix
star
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
nikelle.petrillo
• 0
1
vote
2
replies
1.5k
views
Gviz off-by-one with STAR BAM
gviz
off-by-one
STAR
BAM
coverage
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
bernt.popp
• 0
1
vote
7
replies
5.2k
views
featureCounts creating fragments and high NoFeatures value
featurecounts
bioconductor
differential gene expression
star
updated 7.2 years ago by
Wei Shi
★ 3.6k • written 7.2 years ago by
gregory.l.stone
▴ 10
0
votes
10
replies
4.7k
views
Differential expression analysis for STAR-aligned RNA-Seq data
deseq2
rnaseq
STAR
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
sum31278
• 0
4
votes
7
replies
2.1k
views
RNAseq reads mapped to the gene
star
featurecounts
edgeR
RNAseq
7.8 years ago
myprogramming2016
• 0
0
votes
0
replies
1.1k
views
STAR_how many mismatches to allow if the read length is 100 bp in RNA-seq data
star
8.3 years ago
tg369
▴ 10
1
vote
5
replies
2.2k
views
Single end STAR Chimeric.out.junction fails to read with chimera::importFusionData
chimera
STAR
updated 9.1 years ago by
rcaloger
▴ 500 • written 9.2 years ago by
wresch
• 0
0
votes
5
replies
2.8k
views
Problem Importing STAR fusion data into chimera
fusion genes
chimera
star
updated 9.1 years ago by
richa_r
• 0 • written 9.4 years ago by
am26
• 0
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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