Showing : featurecounts • reset
0
votes
0
replies
271
views
Blank gene_id in featureCounts
featureCounts Rsubread
5 months ago Meg • 0
5
votes
10
replies
2.5k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 11 months ago by • 0
0
votes
1
reply
927
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 8 months ago by 53k • written 8 months ago by ▴ 80
0
votes
1
reply
841
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 10 months ago by 53k • written 20 months ago by • 0
1
vote
3
replies
1.7k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
13 months ago • updated 12 months ago yasmin.hilliam ▴ 10
0
votes
1
reply
616
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
13 months ago isaac.vock • 0
6
votes
5
replies
4.1k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 10 months ago by ▴ 20 • written 14 months ago by • 0
0
votes
4
replies
1.2k
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
15 months ago Jessica • 0
1
vote
2
replies
887
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
15 months ago Anke • 0
4
votes
2
replies
1.9k
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
17 months ago Rachael • 0
2
votes
4
replies
1.5k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
19 months ago • updated 17 months ago isaac.vock • 0
1
vote
1
reply
1.1k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 20 months ago by ★ 3.6k • written 21 months ago by • 0
7
votes
28
replies
8.5k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 21 months ago by 53k • written 10.7 years ago by ★ 7.9k
0
votes
4
replies
1.4k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 21 months ago by 53k • written 21 months ago by • 0
4
votes
6
replies
1.6k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
21 months ago isaac.vock • 0
0
votes
2
replies
4.9k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.3 years ago by ▴ 80
0
votes
0
replies
2.1k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.2 years ago Gordon Smyth 53k
0
votes
2
replies
2.4k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
1
reply
1.2k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.3 years ago by ▴ 450 • written 2.3 years ago by • 0
0
votes
1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.5 years ago by ★ 3.6k • written 2.5 years ago by • 0
0
votes
0
replies
798
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.6 years ago barrypraveen • 0
2
votes
9
replies
3.2k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.7 years ago Hilary ▴ 40
0
votes
2
replies
1.4k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.9 years ago by • 0
0
votes
0
replies
1.1k
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
2.7 years ago yao hua • 0
0
votes
1
reply
1.4k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.8 years ago by ▴ 450 • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
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 2.8 years ago by ★ 1.4k • written 2.8 years ago by • 0
3
votes
3
replies
6.8k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
votes
1
reply
3.9k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 2.9 years ago by ★ 1.4k • written 2.9 years ago by • 0
1
vote
1
reply
3.7k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.9 years ago by 53k • written 3.0 years ago by • 0
0
votes
0
replies
985
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
votes
3
replies
2.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
2
votes
2
replies
1.3k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
3.0 years ago dario.beraldi • 0
0
votes
0
replies
962
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.1 years ago rridley3 • 0
0
votes
2
replies
2.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.2 years ago KMS ▴ 20
0
votes
1
reply
5.2k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
votes
1
reply
1.2k
views
fetaure counts err
featurecounts
updated 3.3 years ago by ★ 3.6k • written 3.3 years ago by • 0
0
votes
1
reply
1.4k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.5 years ago • updated 3.4 years ago NIK • 0
1
vote
1
reply
2.2k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
votes
1
reply
2.3k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by ▴ 10
0
votes
4
replies
2.6k
views
featureCounts: 0% successfully assigned fragments
featureCounts
3.5 years ago KMS ▴ 20
1
vote
4
replies
2.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.5 years ago Chise ▴ 10
3
votes
11
replies
5.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.6 years ago • updated 3.5 years ago Sarah_piggy ▴ 10
1
vote
4
replies
2.9k
views
Subread installation
subread featureCounts
3.6 years ago Lucy ▴ 60
1
vote
5
replies
3.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.7 years ago Lucy ▴ 60
2
votes
2
replies
8.4k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.9 years ago Chise ▴ 10
4
votes
4
replies
6.7k
views
FeatureCounts
counts subread RNASeq featurecounts
4.0 years ago k___ ▴ 30
0
votes
2
replies
2.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.1 years ago by • 0 • written 4.2 years ago by • 0
1
vote
1
reply
1.8k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 4.3 years ago by ★ 3.6k • written 4.3 years ago by • 0
1
vote
5
replies
7.3k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 2.3 years ago by ▴ 450 • written 4.4 years ago by ▴ 10
4
votes
5
replies
3.0k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
4.4 years ago • updated 4.3 years ago Konstantinos Yeles ▴ 90
136 results • Page 1 of 3
Recent ...
Replies
Comment: Save the Date for EuroBioC2026 in Turku! by jamesbennettki • 0
That sounds amazing I have always wanted to visit Finland and meet others in the Bioconductor community Events like EuroBioC2026 inspire me…
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Answer: Integration: Paired-end vs healthy single-end from a different source by James W. MacDonald 68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Awards • All
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
Popular Question to Fred Hutch (Recruiting) ▴ 40
Popular Question to shepherl 4.2k
Locations • All
Qatar, 15 minutes ago
United States, 20 minutes ago
The city by the bay, 31 minutes ago
United States, 48 minutes ago
United States, 1 hour ago
Traffic: 783 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