Showing : featurecounts • reset
0
votes
2
replies
237
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
25 days ago • updated 6 days ago isaac.vock • 0
0
votes
0
replies
132
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
7 weeks ago chris2.a.white • 0
1
vote
1
reply
246
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 7 weeks ago by ★ 3.6k • written 11 weeks ago by • 0
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 11 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
0
votes
4
replies
411
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
4
votes
6
replies
734
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
3 months ago • updated 12 weeks ago isaac.vock • 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
0
votes
0
replies
926
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
8 months ago • updated 7 months ago Gordon Smyth 50k
0
votes
2
replies
997
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
1
vote
1
reply
648
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
0
votes
1
reply
850
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 11 months ago by ★ 3.6k • written 12 months ago by • 0
0
votes
0
replies
416
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
12 months ago barrypraveen • 0
2
votes
9
replies
1.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
13 months ago Hilary ▴ 30
0
votes
2
replies
844
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 13 months ago by ★ 3.6k • written 17 months ago by • 0
0
votes
0
replies
614
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
14 months ago yao hua • 0
0
votes
1
reply
765
views
Subread installation on Linux ARM64
subread featureCounts
updated 14 months ago by ▴ 380 • written 14 months ago by • 0
0
votes
1
reply
542
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 15 months ago by ★ 1.3k • written 15 months ago by • 0
3
votes
3
replies
2.7k
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
0
votes
1
reply
1.9k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 16 months ago by ★ 1.3k • written 16 months ago by • 0
1
vote
1
reply
1.9k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 17 months ago by 50k • written 17 months ago by • 0
0
votes
0
replies
571
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
2
votes
3
replies
1.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 17 months ago by 50k • written 17 months ago by • 0
2
votes
2
replies
760
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
18 months ago dario.beraldi • 0
0
votes
0
replies
522
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
18 months ago rridley3 • 0
0
votes
2
replies
1.4k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
19 months ago KMS ▴ 20
0
votes
1
reply
3.2k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 21 months ago by 50k • written 21 months ago by • 0
0
votes
1
reply
726
views
fetaure counts err
featurecounts
updated 21 months ago by ★ 3.6k • written 21 months ago by • 0
0
votes
1
reply
823
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
23 months ago NIK • 0
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 23 months ago by 50k • written 23 months ago by • 0
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by ▴ 10
0
votes
4
replies
1.7k
views
featureCounts: 0% successfully assigned fragments
featureCounts
23 months ago KMS ▴ 20
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
24 months ago Chise ▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago • updated 24 months ago Sarah_piggy ▴ 10
1
vote
4
replies
1.6k
views
Subread installation
subread featureCounts
2.0 years ago Lucy ▴ 60
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
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
4
replies
4.9k
views
FeatureCounts
counts subread RNASeq featurecounts
2.5 years ago k___ ▴ 30
0
votes
2
replies
1.4k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 18 months ago by • 0 • written 2.7 years ago by • 0
1
vote
1
reply
1.2k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.7 years ago by • 0
1
vote
5
replies
4.7k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 9 months ago by ▴ 380 • written 2.8 years ago by ▴ 10
4
votes
5
replies
2.1k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.9 years ago • updated 2.8 years ago Konstantinos Yeles ▴ 80
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
0
votes
0
replies
764
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
3.5 years ago martinag.work • 0
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
2
votes
3
replies
1.9k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
4
votes
2
replies
1.2k
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by • 0
0
votes
2
replies
1.0k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.7 years ago by ★ 3.6k • written 4.7 years ago by • 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
1
vote
2
replies
2.7k
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
1
vote
1
reply
875
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
Canada, 12 minutes ago
France, 17 minutes ago
United States, 18 minutes ago
United States, 19 minutes ago
United States, 20 minutes ago
Traffic: 1039 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