Showing : FeatureCounts • reset
3
votes
16
replies
17k
views
featureCounts - paired-end data
featurecounts rsubread
updated 10 months ago by • 0 • written 8.9 years ago by ▴ 140
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
2
votes
14
replies
7.5k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 13 months ago by • 0 • written 6.7 years ago by ▴ 110
7
votes
4
replies
6.9k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
9.0 years ago beiting ▴ 30
3
votes
7
replies
6.3k
views
featureCounts simple (borderline stupid...) question
featurecounts
9.2 years ago Sylvain Foisy ▴ 70
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
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
4
votes
6
replies
5.9k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 18 months ago by ▴ 20 • written 5.9 years ago by ▴ 10
2
votes
2
replies
5.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.3 years ago Chise ▴ 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
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
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
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
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
3
votes
5
replies
4.8k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 9.2 years ago by ▴ 380 • written 9.2 years ago by ▴ 20
4
votes
4
replies
4.8k
views
FeatureCounts
counts subread RNASeq featurecounts
2.4 years ago k___ ▴ 30
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
1
vote
5
replies
4.6k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 8 months ago by ▴ 380 • written 2.8 years ago by ▴ 10
4
votes
2
replies
4.5k
views
featureCounts for multiple features
featurecounts
updated 17 months ago by ▴ 20 • written 5.8 years ago by ▴ 10
4
votes
3
replies
4.3k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.7 years ago by ★ 3.6k • written 4.8 years ago by ▴ 80
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
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
0
votes
2
replies
3.9k
views
Problem running featurecounts in Rsubread on GFF file
rsubread featurecounts gff Grch38.p7 vs hg38
6.9 years ago raf4 ▴ 20
5
votes
11
replies
3.8k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 2.0 years ago by ▴ 10 • written 5.0 years ago by ▴ 120
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
2
replies
3.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.1 years ago chatterjee.arumoy ▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago • updated 23 months ago Sarah_piggy ▴ 10
0
votes
2
replies
3.4k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.7 years ago by ▴ 80
0
votes
2
replies
3.4k
views
DEXSeq on FeatureCounts output
dexseq featurecounts
8.6 years ago Vivek.b ▴ 100
0
votes
8
replies
3.3k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread featurecounts
5.9 years ago connor.geraghty • 0
0
votes
4
replies
3.2k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
6.0 years ago octopuslegs11 • 0
0
votes
1
reply
3.1k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 21 months ago by 50k • written 21 months ago by • 0
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
0
votes
6
replies
3.0k
views
Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
deseq2 featurecounts error message
updated 5.6 years ago by 41k • written 5.6 years ago by • 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
13
replies
2.9k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
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
1
vote
1
reply
2.9k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 5.0 years ago by ★ 3.6k • written 5.0 years ago by ▴ 10
0
votes
9
replies
2.8k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 5.4 years ago by ★ 3.6k • written 5.4 years ago by ▴ 40
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
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
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
1
vote
2
replies
2.6k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 4.8 years ago by 50k • written 4.8 years ago by • 0
3
votes
3
replies
2.6k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 15 months ago by 50k • written 15 months ago by • 0
4
votes
7
replies
2.6k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 20
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
1
vote
1
reply
2.5k
views
Warning using feuture count related to GTF file
featurecounts
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
3
replies
2.5k
views
featureCount and bam
featurecounts
6.8 years ago Morris ▴ 10
0
votes
7
replies
2.4k
views
caught segfault when using featureCounts
rsubread featurecounts
6.3 years ago Ge Tan ▴ 20
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
50 results • Page 1 of 1
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Comment: Interaction Terms in DESeq2 - Shrinkage by Michael Love 41k
Yes, apeglm requires relevel and nbinomWaldTest to generate the coefficient estimate and its SE. Alternatively you can use ashr with a con…
Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0
Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Answer: blockwiseModule crashes in the end and doesn't generate modules by xaweh28128 • 0
Test your word skills and see if you can crack the code in today's Wordle puzzle. [Nytimes wordle](https://wordlenytimes.net/quordle-game/)…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
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