Showing : featureCounts • reset
2
votes
16
replies
15k
views
featureCounts - paired-end data
featurecounts rsubread
updated 3 months ago by • 0 • written 8.4 years ago by ▴ 140
7
votes
6
replies
15k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 8.8 years ago by 63k • written 8.8 years ago by ▴ 10
2
votes
14
replies
6.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 7 months ago by • 0 • written 6.1 years ago by ▴ 110
7
votes
4
replies
6.6k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
8.4 years ago beiting ▴ 30
3
votes
7
replies
6.0k
views
featureCounts simple (borderline stupid...) question
featurecounts
8.6 years ago Sylvain Foisy ▴ 50
4
votes
5
replies
5.5k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 7.3 years ago by ★ 3.5k • written 7.4 years ago by ▴ 180
4
votes
6
replies
5.1k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 11 months ago by ▴ 20 • written 5.4 years ago by ▴ 10
0
votes
4
replies
4.9k
views
summaries featureCounts output for egeR
featurecounts edger
updated 7.6 years ago by ★ 3.5k • written 7.6 years ago by • 0
6
votes
26
replies
4.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.8 years ago by ▴ 380 • written 8.5 years ago by 7.8k
4
votes
3
replies
4.8k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 5.9 years ago by ★ 3.5k • written 5.9 years ago by ▴ 80
2
votes
4
replies
4.7k
views
featureCounts (sourceforge) not returning any counts in count table, even though summary indicates reads were assigned?
featurecounts software error
7.6 years ago Darya Vanichkina ▴ 120
1
vote
7
replies
4.7k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 6.6 years ago by ★ 3.5k • written 6.6 years ago by ▴ 10
3
votes
6
replies
4.6k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 21 months ago by 48k • written 6.9 years ago by ▴ 20
3
votes
5
replies
4.4k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 8.6 years ago by ▴ 380 • written 8.6 years ago by ▴ 20
2
votes
2
replies
4.2k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
21 months ago Chise ▴ 10
4
votes
3
replies
4.2k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
8.9 years ago gustavoborin01 • 0
4
votes
2
replies
3.9k
views
featureCounts for multiple features
featurecounts
updated 10 months ago by ▴ 20 • written 5.2 years ago by ▴ 10
4
votes
3
replies
3.8k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.2 years ago by ★ 3.5k • written 4.2 years ago by ▴ 80
4
votes
15
replies
3.7k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 5.8 years ago by 40k • written 5.9 years ago by ▴ 10
3
votes
3
replies
3.6k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
8.6 years ago samuel collombet ▴ 140
0
votes
2
replies
3.6k
views
Problem running featurecounts in Rsubread on GFF file
rsubread featurecounts gff Grch38.p7 vs hg38
6.3 years ago raf4 ▴ 20
4
votes
4
replies
3.6k
views
FeatureCounts
counts subread RNASeq featurecounts
22 months ago k___ ▴ 20
1
vote
5
replies
3.5k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 8 weeks ago by ▴ 380 • written 2.2 years ago by ▴ 10
5
votes
11
replies
3.2k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 17 months ago by ▴ 10 • written 4.4 years ago by ▴ 120
7
votes
5
replies
3.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 4.5 years ago by 48k • written 4.5 years ago by ▴ 60
0
votes
2
replies
3.1k
views
DEXSeq on FeatureCounts output
dexseq featurecounts
8.0 years ago Vivek.b ▴ 100
1
vote
2
replies
2.9k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
3.5 years ago chatterjee.arumoy ▴ 10
0
votes
4
replies
2.9k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
5.4 years ago octopuslegs11 • 0
0
votes
1
reply
2.8k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
updated 3.2 years ago by ★ 1.3k • written 3.2 years ago by ▴ 80
3
votes
2
replies
2.7k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 5.2 years ago by 48k • written 5.2 years ago by • 0
0
votes
8
replies
2.7k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread featurecounts
5.3 years ago connor.geraghty • 0
1
vote
5
replies
2.6k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 6.1 years ago by 63k • written 6.1 years ago by • 0
0
votes
3
replies
2.6k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread featurecounts exon mRNAseq
updated 6.3 years ago by ★ 3.5k • written 6.3 years ago by ▴ 10
3
votes
11
replies
2.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
17 months ago • updated 16 months ago Sarah_piggy ▴ 10
0
votes
6
replies
2.5k
views
Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
deseq2 featurecounts error message
updated 5.1 years ago by 40k • written 5.1 years ago by • 0
9
votes
4
replies
2.5k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
8.8 years ago Wei Shi ★ 3.5k
0
votes
2
replies
2.5k
views
lncRNA annotation for featureCouns and STAR
lncRNA featureCounts STAR annotation
updated 5.3 years ago by ★ 3.5k • written 5.3 years ago by ▴ 10
2
votes
2
replies
2.5k
views
featureCounts Parameters for Exon Junctions
rsubread featureCounts
updated 6.9 years ago by ★ 3.5k • written 6.9 years ago by ★ 1.5k
3
votes
13
replies
2.4k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 4.7 years ago by 48k • written 4.7 years ago by • 0
1
vote
1
reply
2.4k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 4.5 years ago by ★ 3.5k • written 4.5 years ago by ▴ 10
0
votes
9
replies
2.4k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 4.8 years ago by ★ 3.5k • written 4.8 years ago by ▴ 40
1
vote
1
reply
2.3k
views
Warning using feuture count related to GTF file
featurecounts
updated 5.0 years ago by 63k • written 5.0 years ago by • 0
4
votes
7
replies
2.3k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 5.3 years ago by 40k • written 5.3 years ago by ▴ 20
3
votes
1
reply
2.1k
views
Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 5.9 years ago by ★ 3.5k • written 5.9 years ago by • 0
0
votes
3
replies
2.1k
views
featureCount and bam
featurecounts
6.2 years ago Morris ▴ 10
0
votes
7
replies
2.1k
views
caught segfault when using featureCounts
rsubread featurecounts
5.8 years ago Ge Tan ▴ 20
3
votes
2
replies
2.1k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread featurecounts
updated 6.4 years ago by ★ 3.5k • written 6.4 years ago by ▴ 70
1
vote
2
replies
2.1k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 4.2 years ago by 48k • written 4.2 years ago by • 0
0
votes
1
reply
2.0k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 14 months ago by 48k • written 14 months ago by • 0
0
votes
5
replies
1.9k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 10 weeks ago by ▴ 380 • written 6.4 years ago by • 0
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Answer: DelayedArray::read_sparse_block by Hervé Pagès 16k
Hi Koki, Sorry again for the slow response. `read_sparse_block()` has been around for years. It's a generic function defined in the *…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Votes
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
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