Showing : FeatureCounts • reset
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Clarification on counting in Rsubread (featureCounts)
featureCounts Rsubread
updated 42 minutes ago by 53k • written 28 days ago by • 0
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322
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Blank gene_id in featureCounts
featureCounts Rsubread
7 months ago Meg • 0
5
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10
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2.7k
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Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 13 months ago by • 0
0
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1
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1.1k
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 11 months ago by 53k • written 11 months ago by ▴ 80
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1
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929
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Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 13 months ago by 53k • written 22 months ago by • 0
1
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3
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2.0k
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featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
15 months ago yasmin.hilliam ▴ 10
0
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1
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719
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[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
15 months ago isaac.vock • 0
6
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5
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4.5k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 12 months ago by ▴ 20 • written 17 months ago by • 0
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4
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1.3k
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
18 months ago • updated 17 months ago Jessica • 0
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990
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
17 months ago Anke • 0
4
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2
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2.2k
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
19 months ago Rachael • 0
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4
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1.7k
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
21 months ago • updated 19 months ago isaac.vock • 0
1
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1
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1.2k
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 22 months ago by ★ 3.6k • written 23 months ago by • 0
7
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28
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8.8k
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Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 23 months ago by 53k • written 10.8 years ago by ★ 7.9k
0
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4
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1.6k
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Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 23 months ago by 53k • written 23 months ago by • 0
4
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6
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1.7k
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[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
23 months ago isaac.vock • 0
0
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2
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5.1k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.5 years ago by ▴ 80
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0
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2.2k
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.4 years ago Gordon Smyth 53k
0
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2
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2.6k
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
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1
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1.3k
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featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.5 years ago by ▴ 450 • written 2.5 years ago by • 0
0
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1
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1.6k
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Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.7 years ago by • 0
0
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0
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853
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.8 years ago barrypraveen • 0
2
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9
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3.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.9 years ago • updated 2.8 years ago Hilary ▴ 40
0
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2
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1.5k
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.9 years ago by ★ 3.6k • written 3.1 years ago by • 0
0
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0
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1.2k
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
2.9 years ago yao hua • 0
0
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1
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1.6k
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Subread installation on Linux ARM64
subread featureCounts
updated 2.9 years ago by ▴ 450 • written 2.9 years ago by • 0
0
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1
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1.1k
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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 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
3
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3
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7.1k
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
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1
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4.0k
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
1
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1
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3.9k
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Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
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0
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1.0k
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Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
2
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3
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2.5k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
2
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2
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1.4k
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featureCounts: No effect of setting -d and -D?
subread featureCounts
3.2 years ago dario.beraldi • 0
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0
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1.0k
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.2 years ago rridley3 • 0
0
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2
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2.7k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.4 years ago KMS ▴ 20
0
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1
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5.4k
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gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
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1
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1.3k
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fetaure counts err
featurecounts
updated 3.5 years ago by ★ 3.6k • written 3.5 years ago by • 0
0
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1
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1.5k
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.6 years ago NIK • 0
1
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1
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2.3k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
2
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1
reply
2.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by ▴ 10
0
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4
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2.7k
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featureCounts: 0% successfully assigned fragments
featureCounts
3.7 years ago KMS ▴ 20
1
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4
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2.5k
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Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.7 years ago Chise ▴ 10
3
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11
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5.9k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.7 years ago Sarah_piggy ▴ 10
1
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4
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3.0k
views
Subread installation
subread featureCounts
3.8 years ago Lucy ▴ 60
1
vote
5
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3.5k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.9 years ago Lucy ▴ 60
2
votes
2
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8.6k
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"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
4.1 years ago • updated 4.0 years ago Chise ▴ 10
4
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4
replies
6.8k
views
FeatureCounts
counts subread RNASeq featurecounts
4.2 years ago k___ ▴ 30
0
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2
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2.2k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.3 years ago by • 0 • written 4.4 years ago by • 0
1
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1
reply
1.9k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 4.4 years ago by ★ 3.6k • written 4.4 years ago by • 0
1
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5
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7.5k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 2.5 years ago by ▴ 450 • written 4.5 years ago by ▴ 10
137 results • Page 1 of 3
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Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
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