Showing : FeatureCounts • reset
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 10 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
4
votes
3
replies
4.6k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
9.5 years ago gustavoborin01 • 0
6
votes
4
replies
1.3k
views
Aggregate read counts by non-uniform overlapping sliding windows
granges genomicranges featurecounts
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 20
0
votes
4
replies
5.1k
views
summaries featureCounts output for egeR
featurecounts edger
updated 8.2 years ago by ★ 3.6k • written 8.2 years ago by • 0
3
votes
3
replies
4.0k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
9.2 years ago • updated 9.1 years ago samuel collombet ▴ 140
3
votes
7
replies
6.3k
views
featureCounts simple (borderline stupid...) question
featurecounts
9.2 years ago Sylvain Foisy ▴ 70
3
votes
2
replies
3.1k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 5.8 years ago by 50k • written 5.8 years ago by • 0
4
votes
5
replies
1.4k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts rnaseq subread
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
2
votes
2
replies
1.8k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.1 years ago by ▴ 380 • written 3.1 years ago by • 0
7
votes
4
replies
6.9k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
9.0 years ago beiting ▴ 30
1
vote
4
replies
1.7k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 6.1 years ago by ★ 3.6k • written 6.2 years ago by • 0
0
votes
3
replies
1.9k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
9.3 years ago ccheung • 0
4
votes
3
replies
4.3k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.8 years ago by ★ 3.6k • written 4.8 years ago by ▴ 80
7
votes
5
replies
3.7k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 60
1
vote
7
replies
5.3k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 7.2 years ago by ★ 3.6k • written 7.2 years ago by ▴ 10
3
votes
7
replies
1.9k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 5.0 years ago by 50k • written 5.0 years ago by • 0
9
votes
4
replies
2.8k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
9.4 years ago Wei Shi ★ 3.6k
4
votes
6
replies
724
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
12 weeks ago • updated 11 weeks ago isaac.vock • 0
4
votes
5
replies
6.0k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 7.9 years ago by ★ 3.6k • written 8.0 years ago by ▴ 180
2
votes
14
replies
7.5k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 14 months ago by • 0 • written 6.7 years ago by ▴ 110
4
votes
7
replies
2.1k
views
RNAseq reads mapped to the gene
star featurecounts edgeR RNAseq
7.9 years ago myprogramming2016 • 0
0
votes
5
replies
1.8k
views
Rsubread, featureCounts misses some exons
annotation featurecounts rsubread
updated 8.6 years ago by 50k • written 8.6 years ago by ▴ 80
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts rsubread
updated 10 months ago by • 0 • written 8.9 years ago by ▴ 140
0
votes
2
replies
2.9k
views
lncRNA annotation for featureCouns and STAR
lncRNA featureCounts STAR annotation
updated 5.9 years ago by ★ 3.6k • written 5.9 years ago by ▴ 10
2
votes
4
replies
1.4k
views
featureCounts to RangedSummarizedExperiment
windowcounts featurecounts
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
1
vote
2
replies
1.0k
views
DEseq2 analysis for 2 batches of samples that are sequenced separately
deseq2 featurecounts rnaseq
updated 7.7 years ago by 65k • written 7.7 years ago by ▴ 20
3
votes
5
replies
1.7k
views
Can featurecounts count number of mapped reads rapidly in arbitrary regions?
featurecounts rsubread
7.8 years ago Hadi Gharibi • 0
3
votes
6
replies
5.3k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 2.3 years ago by 50k • written 7.5 years ago by ▴ 20
2
votes
2
replies
2.8k
views
featureCounts Parameters for Exon Junctions
rsubread featureCounts
updated 7.5 years ago by ★ 3.6k • written 7.5 years ago by ★ 1.5k
3
votes
2
replies
2.4k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread featurecounts
updated 7.0 years ago by ★ 3.6k • written 7.0 years ago by ▴ 70
3
votes
1
reply
2.5k
views
Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 6.5 years ago by ★ 3.6k • written 6.5 years ago by • 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 18 days ago by • 0 • written 7.8 years ago by ▴ 90
2
votes
1
reply
1.0k
views
Are the endpoints included in intervals for SAF format?
rsubread featurecounts saf
8.9 years ago Ryan C. Thompson ★ 7.9k
2
votes
3
replies
1.4k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 13 months ago by 50k • written 5.9 years ago by ▴ 20
1
vote
1
reply
1.9k
views
featureCounts using 3'UTR as genome
featurecounts R
updated 6.7 years ago by 65k • written 6.7 years ago by • 0
0
votes
6
replies
1.9k
views
Rsubread featureCounts with byReadGroup
rsubread featurecounts
updated 6.5 years ago by ▴ 380 • written 6.6 years ago by ▴ 20
0
votes
4
replies
3.2k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
6.0 years ago octopuslegs11 • 0
1
vote
5
replies
3.0k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 6.7 years ago by 65k • written 6.7 years ago by • 0
3
votes
3
replies
1.9k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 8.0 years ago by ★ 13k • written 8.0 years ago by • 0
0
votes
3
replies
2.8k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread featurecounts exon mRNAseq
updated 6.9 years ago by ★ 3.6k • written 6.9 years ago by ▴ 10
0
votes
2
replies
1.1k
views
negative value for minOverlap parameter
Rsubread minOverlap featureCounts
updated 8.0 years ago by ★ 3.6k • written 8.0 years ago by • 0
7
votes
6
replies
16k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 9.3 years ago by 65k • written 9.3 years ago by ▴ 10
4
votes
6
replies
6.0k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 18 months ago by ▴ 20 • written 5.9 years ago by ▴ 10
4
votes
3
replies
5.5k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 6.4 years ago by ★ 3.6k • written 6.4 years ago by ▴ 80
0
votes
7
replies
2.4k
views
caught segfault when using featureCounts
rsubread featurecounts
6.3 years ago Ge Tan ▴ 20
4
votes
8
replies
1.4k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
0
votes
3
replies
1.3k
views
FeatureCounts --read2pos option
featurecounts
updated 7.1 years ago by ★ 3.6k • written 7.1 years ago by • 0
3
votes
1
reply
1.2k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq annotation featurecounts biomart
updated 6.5 years ago by 65k • written 6.5 years ago by • 0
4
votes
15
replies
4.2k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 6.4 years ago by 41k • written 6.5 years ago by ▴ 10
2
votes
4
replies
5.0k
views
featureCounts (sourceforge) not returning any counts in count table, even though summary indicates reads were assigned?
featurecounts software error
8.2 years ago Darya Vanichkina ▴ 120
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Awards • All
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Popular Question to W. Evan Johnson ▴ 850
Popular Question to Alejandro Reyes ★ 1.9k
Locations • All
China, 14 minutes ago
United States, 15 minutes ago
WEHI, Melbourne, Australia, 28 minutes ago
The city by the bay, 42 minutes ago
France, 49 minutes ago
Traffic: 552 users visited in the last hour
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