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reset
4
votes
7
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2.1k
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RNAseq reads mapped to the gene
star
featurecounts
edgeR
RNAseq
7.9 years ago
myprogramming2016
• 0
3
votes
2
replies
2.1k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq
featureCounts
STAR
minMQS
mapping quality score
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
Gary
▴ 20
2
votes
2
replies
1.1k
views
Why does total unique map not equal to library size?
htseqcounts
star
rnaseq
6.7 years ago
Ahdee
▴ 50
2
votes
3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
2
votes
2
replies
7.3k
views
RNA STAR to DESeq2
deseq2
count matrix
star
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
nikelle.petrillo
• 0
1
vote
3
replies
1.5k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
josephbrown
▴ 10
1
vote
5
replies
2.2k
views
Single end STAR Chimeric.out.junction fails to read with chimera::importFusionData
chimera
STAR
updated 9.2 years ago by
rcaloger
▴ 500 • written 9.3 years ago by
wresch
• 0
1
vote
7
replies
5.3k
views
featureCounts creating fragments and high NoFeatures value
featurecounts
bioconductor
differential gene expression
star
updated 7.3 years ago by
Wei Shi
★ 3.6k • written 7.3 years ago by
gregory.l.stone
▴ 10
1
vote
2
replies
1.5k
views
Gviz off-by-one with STAR BAM
gviz
off-by-one
STAR
BAM
coverage
updated 7.1 years ago by
Martin Morgan
25k • written 7.1 years ago by
bernt.popp
• 0
0
votes
10
replies
4.7k
views
Differential expression analysis for STAR-aligned RNA-Seq data
deseq2
rnaseq
STAR
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
sum31278
• 0
0
votes
2
replies
1.1k
views
BAM file into R from Illumina
bam file
STAR
Illumina
updated 6.0 years ago by
ta_awwad
▴ 10 • written 6.0 years ago by
soheilazareie
• 0
0
votes
2
replies
2.9k
views
lncRNA annotation for featureCouns and STAR
lncRNA
featureCounts
STAR
annotation
updated 5.9 years ago by
Wei Shi
★ 3.6k • written 5.9 years ago by
inah
▴ 10
0
votes
3
replies
3.3k
views
Handling pseudogenes in RNA-seq
rna-seq
pseudogenes
STAR
counts
updated 5.9 years ago by
Levi Waldron
★ 1.1k • written 5.9 years ago by
supremerulersuraj
• 0
0
votes
1
reply
910
views
weired output with featurecount
featurecounts
star
5.6 years ago
roghaiyeh.safari
• 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
8.4 years ago
tg369
▴ 10
0
votes
1
reply
893
views
Using STAR and DESeq2 for circRNA analysis
STAR
deseq2
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
csijst
• 0
0
votes
1
reply
1.7k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
mohamedrefaat.1.1992
• 0
0
votes
1
reply
1.9k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads
STAR
featureCounts
updated 17 months ago by
swbarnes2
★ 1.3k • written 17 months ago by
lalala
• 0
0
votes
1
reply
584
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 15 months ago by
Michael Love
41k • written 16 months ago by
nico
• 0
0
votes
5
replies
2.9k
views
Problem Importing STAR fusion data into chimera
fusion genes
chimera
star
updated 9.2 years ago by
richa_r
• 0 • written 9.5 years ago by
am26
• 0
20 results • Page
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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