Showing : FeatureCounts • reset
4
votes
2
replies
211
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
21 days ago • updated 20 days ago Rachael • 0
2
votes
4
replies
626
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
3 months ago • updated 19 days ago isaac.vock • 0
0
votes
0
replies
203
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
4 months ago chris2.a.white • 0
1
vote
1
reply
356
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 4 months ago by ★ 3.6k • written 4 months ago by • 0
7
votes
28
replies
6.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 5 months ago by 51k • written 9.3 years ago by ★ 7.9k
0
votes
4
replies
537
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 5 months ago by 51k • written 5 months ago by • 0
4
votes
6
replies
847
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
5 months ago isaac.vock • 0
0
votes
2
replies
3.7k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.0 years ago by ▴ 80
0
votes
0
replies
1.1k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
10 months ago Gordon Smyth 51k
0
votes
2
replies
1.2k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 11 months ago by 66k • written 11 months ago by • 0
1
vote
1
reply
728
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 11 months ago by ▴ 440 • written 11 months ago by • 0
0
votes
1
reply
951
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 14 months ago by ★ 3.6k • written 14 months ago by • 0
0
votes
0
replies
458
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
14 months ago barrypraveen • 0
2
votes
9
replies
1.8k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
16 months ago Hilary ▴ 30
0
votes
2
replies
926
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 16 months ago by ★ 3.6k • written 19 months ago by • 0
0
votes
0
replies
685
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
16 months ago yao hua • 0
0
votes
1
reply
867
views
Subread installation on Linux ARM64
subread featureCounts
updated 17 months ago by ▴ 440 • written 17 months ago by • 0
0
votes
1
reply
636
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 17 months ago by ★ 1.4k • written 17 months ago by • 0
3
votes
3
replies
3.2k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 17 months ago by 51k • written 17 months ago by • 0
0
votes
1
reply
2.2k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
1
vote
1
reply
2.1k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 19 months ago by 51k • written 19 months ago by • 0
0
votes
0
replies
615
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 19 months ago by ★ 4.2k • written 19 months ago by • 0
2
votes
3
replies
1.4k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 20 months ago by 51k • written 20 months ago by • 0
2
votes
2
replies
830
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
20 months ago dario.beraldi • 0
0
votes
0
replies
570
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
20 months ago rridley3 • 0
0
votes
2
replies
1.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
22 months ago KMS ▴ 20
0
votes
1
reply
3.5k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 24 months ago by 51k • written 24 months ago by • 0
0
votes
1
reply
811
views
fetaure counts err
featurecounts
updated 23 months ago by ★ 3.6k • written 24 months ago by • 0
0
votes
1
reply
933
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.1 years ago NIK • 0
1
vote
1
reply
1.5k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.1 years ago by 51k • written 2.1 years ago by • 0
2
votes
1
reply
1.6k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by ▴ 10
0
votes
4
replies
1.9k
views
featureCounts: 0% successfully assigned fragments
featureCounts
2.1 years ago KMS ▴ 20
1
vote
4
replies
1.6k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.2 years ago Chise ▴ 10
3
votes
11
replies
3.8k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.2 years ago Sarah_piggy ▴ 10
1
vote
4
replies
1.8k
views
Subread installation
subread featureCounts
2.2 years ago Lucy ▴ 60
1
vote
5
replies
2.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.4 years ago Lucy ▴ 60
2
votes
2
replies
6.3k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.5 years ago Chise ▴ 10
4
votes
4
replies
5.2k
views
FeatureCounts
counts subread RNASeq featurecounts
2.6 years ago k___ ▴ 30
0
votes
2
replies
1.5k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 21 months ago by • 0 • written 2.9 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 2.9 years ago by ★ 3.6k • written 2.9 years ago by • 0
1
vote
5
replies
5.0k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 11 months ago by ▴ 440 • written 3.0 years ago by ▴ 10
4
votes
5
replies
2.2k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
3.1 years ago • updated 3.0 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.9k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.3 years ago by ▴ 440 • written 3.3 years ago by • 0
0
votes
0
replies
808
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
3.7 years ago martinag.work • 0
1
vote
2
replies
3.7k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.3 years ago chatterjee.arumoy ▴ 10
2
votes
3
replies
2.0k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 4.6 years ago by 66k • written 4.6 years ago by • 0
4
votes
2
replies
1.3k
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
0
votes
2
replies
1.1k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.9 years ago by ★ 3.6k • written 4.9 years ago by • 0
4
votes
3
replies
4.5k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 5.0 years ago by ★ 3.6k • written 5.0 years ago by ▴ 80
1
vote
2
replies
2.9k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 5.0 years ago by 51k • written 5.0 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Awards • All
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to ATpoint ★ 4.2k
Popular Question to WouterDeCoster ▴ 130
Scholar to Gordon Smyth 51k
Voter to Chris ▴ 20
Locations • All
Netherlands, 3 minutes ago
United States, 8 minutes ago
Philippines, 12 minutes ago
St Louis, MO, 17 minutes ago
United States, 21 minutes ago
Traffic: 1183 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