Showing : featureCounts • reset
0
votes
0
replies
157
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
23 days ago • updated 20 days ago Gordon Smyth 48k
0
votes
2
replies
207
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 6 weeks ago by 63k • written 6 weeks ago by • 0
1
vote
1
reply
262
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 weeks ago by ▴ 380 • written 9 weeks ago by • 0
0
votes
1
reply
332
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 4 months ago by ★ 3.5k • written 4 months ago by • 0
0
votes
0
replies
202
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
5 months ago barrypraveen • 0
2
votes
9
replies
831
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
6 months ago Hilary ▴ 30
0
votes
0
replies
252
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
7 months ago yao hua • 0
0
votes
1
reply
402
views
Subread installation on Linux ARM64
subread featureCounts
updated 7 months ago by ▴ 380 • written 7 months ago by • 0
0
votes
1
reply
276
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2 featurecounts
updated 7 months ago by ★ 1.3k • written 7 months ago by • 0
3
votes
3
replies
1.2k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 8 months ago by 48k • written 8 months ago by • 0
0
votes
1
reply
992
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 9 months ago by ★ 1.3k • written 9 months ago by • 0
0
votes
2
replies
492
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 6 months ago by ★ 3.5k • written 9 months ago by • 0
1
vote
1
reply
1.0k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 10 months ago by 48k • written 10 months ago by • 0
0
votes
0
replies
300
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 10 months ago by ★ 3.4k • written 10 months ago by • 0
2
votes
3
replies
651
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 10 months ago by 48k • written 10 months ago by • 0
2
votes
2
replies
444
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
11 months ago dario.beraldi • 0
0
votes
0
replies
302
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
11 months ago rridley3 • 0
0
votes
2
replies
901
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
12 months ago KMS ▴ 10
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
1
reply
501
views
fetaure counts err
featurecounts
updated 14 months ago by ★ 3.5k • written 14 months ago by • 0
0
votes
1
reply
537
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
16 months ago • updated 15 months ago NIK • 0
1
vote
1
reply
1.0k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 16 months ago by 48k • written 16 months ago by • 0
2
votes
1
reply
1.1k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 10
0
votes
4
replies
1.2k
views
featureCounts: 0% successfully assigned fragments
featureCounts
16 months ago KMS ▴ 10
1
vote
4
replies
944
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
17 months ago • updated 16 months ago Chise ▴ 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
1
vote
4
replies
1.1k
views
Subread installation
subread featureCounts
17 months ago Lucy ▴ 60
1
vote
5
replies
1.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
19 months ago Lucy ▴ 60
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
4
replies
3.6k
views
FeatureCounts
counts subread RNASeq featurecounts
22 months ago k___ ▴ 20
0
votes
2
replies
1.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 11 months ago by • 0 • written 2.1 years ago by • 0
1
vote
1
reply
837
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 2.1 years ago by ★ 3.5k • written 2.1 years ago by • 0
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
4
votes
5
replies
1.6k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.3 years ago • updated 2.2 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.4k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 2.6 years ago by ▴ 380 • written 2.6 years ago by • 0
0
votes
0
replies
542
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
2.9 years ago martinag.work • 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
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
2
votes
3
replies
1.6k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 3.8 years ago by 63k • written 3.8 years ago by • 0
4
votes
2
replies
924
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.0 years ago by ★ 1.3k • written 4.0 years ago by • 0
0
votes
2
replies
813
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.1 years ago by ★ 3.5k • written 4.1 years ago by • 0
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
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
1
vote
1
reply
700
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 40
3
votes
7
replies
1.6k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
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
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
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
2
votes
6
replies
1.5k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 4.5 years ago by ★ 3.5k • written 4.5 years ago by • 0
1
vote
2
replies
1.1k
views
Problem with importing text file in featureCounts
Rsubread featureCounts
updated 4.5 years ago by 48k • written 4.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
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
Awards • All
Popular Question to komal.rathi ▴ 110
Popular Question to Levi Waldron 1.1k
Popular Question to Lucas Schiffer ▴ 240
Popular Question to Ed Siefker ▴ 230
Popular Question to James W. MacDonald 63k
Locations • All
United States, 11 minutes ago
United Kingdom, 12 minutes ago
WEHI, Melbourne, Australia, 36 minutes ago
United States, 37 minutes ago
Singapore, 1 hour ago
Traffic: 572 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