Showing : featureCounts • reset
0
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219
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Blank gene_id in featureCounts
featureCounts Rsubread
4 months ago Meg • 0
5
votes
10
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2.4k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 9 months ago by • 0
0
votes
1
reply
890
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 7 months ago by 53k • written 7 months ago by ▴ 80
0
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1
reply
803
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 9 months ago by 53k • written 19 months ago by • 0
1
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3
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1.6k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
11 months ago yasmin.hilliam ▴ 10
0
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1
reply
579
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[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
12 months ago isaac.vock • 0
6
votes
5
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4.0k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 9 months ago by ▴ 20 • written 13 months ago by • 0
0
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4
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1.1k
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
14 months ago Jessica • 0
1
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2
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858
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
14 months ago Anke • 0
4
votes
2
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1.8k
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
15 months ago Rachael • 0
2
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4
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1.5k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
18 months ago • updated 15 months ago isaac.vock • 0
1
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1
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1.0k
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 19 months ago by ★ 3.6k • written 20 months ago by • 0
7
votes
28
replies
8.3k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 20 months ago by 53k • written 10.6 years ago by ★ 7.9k
0
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4
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1.4k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 20 months ago by 53k • written 20 months ago by • 0
4
votes
6
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1.6k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
20 months ago isaac.vock • 0
0
votes
2
replies
4.8k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.2 years ago by ▴ 80
0
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0
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2.0k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.1 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 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
1
reply
1.2k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.2 years ago by ▴ 450 • written 2.2 years ago by • 0
0
votes
1
reply
1.5k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.4 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
votes
0
replies
773
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.5 years ago barrypraveen • 0
2
votes
9
replies
3.2k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.6 years ago Hilary ▴ 40
0
votes
2
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1.4k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.6 years ago by ★ 3.6k • written 2.8 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
2.6 years ago yao hua • 0
0
votes
1
reply
1.4k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.7 years ago by ▴ 450 • written 2.7 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 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
3
votes
3
replies
6.7k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
0
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1
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3.8k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 2.8 years ago by ★ 1.4k • written 2.8 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 2.9 years ago by • 0
0
votes
0
replies
956
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 2.9 years ago by ★ 4.9k • written 2.9 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 2.9 years ago by 53k • written 2.9 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
907
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.0 years ago rridley3 • 0
0
votes
2
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2.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.1 years ago KMS ▴ 20
0
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1
reply
5.2k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
1
reply
1.2k
views
fetaure counts err
featurecounts
updated 3.2 years ago by ★ 3.6k • written 3.2 years ago by • 0
0
votes
1
reply
1.3k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.4 years ago • updated 3.3 years ago NIK • 0
1
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1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
2
votes
1
reply
2.2k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by ▴ 10
0
votes
4
replies
2.6k
views
featureCounts: 0% successfully assigned fragments
featureCounts
3.4 years ago KMS ▴ 20
1
vote
4
replies
2.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.4 years ago Chise ▴ 10
3
votes
11
replies
5.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.5 years ago • updated 3.4 years ago Sarah_piggy ▴ 10
1
vote
4
replies
2.8k
views
Subread installation
subread featureCounts
3.5 years ago Lucy ▴ 60
1
vote
5
replies
3.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.6 years ago Lucy ▴ 60
2
votes
2
replies
8.4k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.8 years ago Chise ▴ 10
4
votes
4
replies
6.6k
views
FeatureCounts
counts subread RNASeq featurecounts
3.9 years ago k___ ▴ 30
0
votes
2
replies
2.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.0 years ago by • 0 • written 4.1 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 4.2 years ago by ★ 3.6k • written 4.2 years ago by • 0
1
vote
5
replies
7.2k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 2.2 years ago by ▴ 450 • written 4.3 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
4.3 years ago • updated 4.2 years ago Konstantinos Yeles ▴ 90
136 results • Page 1 of 3
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Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
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Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
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