Showing : featureCounts • reset
6
votes
26
replies
5.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 3.0 years ago by ▴ 380 • written 8.8 years ago by 7.8k
2
votes
16
replies
16k
views
featureCounts - paired-end data
featurecounts rsubread
updated 5 months ago by • 0 • written 8.6 years ago by ▴ 140
4
votes
15
replies
3.9k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 6.0 years ago by 41k • written 6.1 years ago by ▴ 10
2
votes
14
replies
6.9k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 9 months ago by • 0 • written 6.3 years ago by ▴ 110
3
votes
13
replies
2.6k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 4.9 years ago by 49k • written 4.9 years ago by • 0
5
votes
11
replies
3.4k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 20 months ago by ▴ 10 • written 4.7 years ago by ▴ 120
3
votes
11
replies
3.0k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
20 months ago • updated 19 months ago Sarah_piggy ▴ 10
0
votes
9
replies
2.5k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 5.0 years ago by ★ 3.5k • written 5.0 years ago by ▴ 40
2
votes
9
replies
1.1k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
9 months ago Hilary ▴ 30
4
votes
8
replies
1.2k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 6.1 years ago by 49k • written 6.1 years ago by • 0
0
votes
8
replies
2.9k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread featurecounts
5.5 years ago connor.geraghty • 0
3
votes
7
replies
1.7k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 4.6 years ago by 49k • written 4.6 years ago by • 0
1
vote
7
replies
4.9k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 6.9 years ago by ★ 3.5k • written 6.9 years ago by ▴ 10
4
votes
7
replies
2.4k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 20
0
votes
7
replies
2.3k
views
caught segfault when using featureCounts
rsubread featurecounts
6.0 years ago Ge Tan ▴ 20
3
votes
7
replies
6.1k
views
featureCounts simple (borderline stupid...) question
featurecounts
8.8 years ago Sylvain Foisy ▴ 50
4
votes
7
replies
1.9k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
7.5 years ago myprogramming2016 • 0
3
votes
6
replies
4.8k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 23 months ago by 49k • written 7.2 years ago by ▴ 20
7
votes
6
replies
15k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 9.0 years ago by 64k • written 9.0 years ago by ▴ 10
0
votes
6
replies
1.3k
views
Options Request for FeatureCounts
featurecounts subread
updated 5.3 years ago by ★ 3.5k • written 5.3 years ago by • 0
2
votes
6
replies
1.6k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 4.7 years ago by ★ 3.5k • written 4.7 years ago by • 0
4
votes
6
replies
5.4k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 14 months ago by ▴ 20 • written 5.6 years ago by ▴ 10
0
votes
6
replies
2.7k
views
Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
deseq2 featurecounts error message
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
0
votes
6
replies
1.7k
views
Rsubread featureCounts with byReadGroup
rsubread featurecounts
updated 6.2 years ago by ▴ 380 • written 6.2 years ago by ▴ 20
0
votes
5
replies
1.7k
views
Rsubread, featureCounts misses some exons
annotation featurecounts rsubread
updated 8.2 years ago by 49k • written 8.2 years ago by ▴ 80
7
votes
5
replies
3.4k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 4.7 years ago by 49k • written 4.7 years ago by ▴ 60
0
votes
5
replies
1.9k
views
featureCounts error : SAM_pairer_iterate_tags
subread featureCounts
updated 4.9 years ago by 49k • written 4.9 years ago by • 0
1
vote
5
replies
1.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
22 months ago Lucy ▴ 60
3
votes
5
replies
1.6k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts rsubread
7.5 years ago Hadi Gharibi • 0
4
votes
5
replies
1.8k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.5 years ago • updated 2.4 years ago Konstantinos Yeles ▴ 80
4
votes
5
replies
5.7k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 7.6 years ago by ★ 3.5k • written 7.6 years ago by ▴ 180
1
vote
5
replies
2.7k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 6.3 years ago by 64k • written 6.3 years ago by • 0
1
vote
5
replies
3.9k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 4 months ago by ▴ 380 • written 2.4 years ago by ▴ 10
0
votes
5
replies
2.1k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 5 months ago by ▴ 380 • written 6.6 years ago by • 0
3
votes
5
replies
4.5k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 8.8 years ago by ▴ 380 • written 8.8 years ago by ▴ 20
4
votes
5
replies
1.2k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts rnaseq subread
updated 5.3 years ago by 49k • written 5.3 years ago by • 0
1
vote
4
replies
1.1k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
19 months ago Chise ▴ 10
2
votes
4
replies
1.3k
views
featureCounts to RangedSummarizedExperiment
windowcounts featurecounts
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
0
votes
4
replies
3.0k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
5.7 years ago octopuslegs11 • 0
7
votes
4
replies
6.7k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
8.7 years ago beiting ▴ 30
0
votes
4
replies
1.4k
views
featureCounts: 0% successfully assigned fragments
featureCounts
19 months ago KMS ▴ 20
1
vote
4
replies
1.2k
views
Subread installation
subread featureCounts
20 months ago Lucy ▴ 60
1
vote
4
replies
1.5k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 5.8 years ago by ★ 3.5k • written 5.8 years ago by • 0
0
votes
4
replies
5.0k
views
summaries featureCounts output for egeR
featurecounts edger
updated 7.8 years ago by ★ 3.5k • written 7.8 years ago by • 0
2
votes
4
replies
4.8k
views
featureCounts (sourceforge) not returning any counts in count table, even though summary indicates reads were assigned?
featurecounts software error
7.9 years ago • updated 7.8 years ago Darya Vanichkina ▴ 120
9
votes
4
replies
2.6k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
9.1 years ago Wei Shi ★ 3.5k
6
votes
4
replies
1.1k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 6.9 years ago by 11k • written 6.9 years ago by ▴ 20
4
votes
4
replies
4.0k
views
FeatureCounts
counts subread RNASeq featurecounts
2.1 years ago k___ ▴ 20
3
votes
3
replies
3.8k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
8.9 years ago • updated 8.8 years ago samuel collombet ▴ 140
4
votes
3
replies
4.3k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
9.1 years ago gustavoborin01 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: biomaRt not working - lazy table error by Mansi • 0
I tried `install("BiocFileCache")` and it installed version 2.6.1. And because I am using R version 4.2.2 so I couldn't upgrade `BiocManage…
Answer: Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DE by James W. MacDonald 64k
The short answer is that you don't. `tximport` is meant to summarize transcript abundance estimates at the gene level, and as you might ima…
Comment: Inconsistent results in DiffBind by ATpoint ★ 3.6k
One is the "raw" logFCs, not corrected for the standard error of the logFCs, the other one the shrunken logFCs from DESeq2 lfcShrink, "corr…
Answer: Can't download Bioconductor by James W. MacDonald 64k
[You need to update][1]. [1]: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#basic-use
Comment: Can't download Bioconductor by ATpoint ★ 3.6k
Please see especially the 1st and 2nd point in https://www.bioconductor.org/help/support/posting-guide/#keypoints
Votes
Answer: biomaRt not working - lazy table error
Answer: biomaRt not working - lazy table error
Answer: biomaRt not working - lazy table error
Answer: Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DE
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
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