Showing : featureCounts • reset
0
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547
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 16 days ago by 52k • written 17 days ago by ▴ 80
4
votes
8
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1.2k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
12 weeks ago • updated 10 weeks ago chris2.a.white • 0
0
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1
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572
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 11 weeks ago by 52k • written 12 months ago by • 0
1
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3
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827
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
4 months ago yasmin.hilliam ▴ 10
0
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1
reply
337
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
5 months ago isaac.vock • 0
6
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5
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2.4k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 8 weeks ago by ▴ 20 • written 6 months ago by • 0
0
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4
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847
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
7 months ago • updated 6 months ago Jessica • 0
1
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2
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610
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
7 months ago Anke • 0
4
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2
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1.0k
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
8 months ago Rachael • 0
2
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4
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1.1k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
11 months ago • updated 8 months ago isaac.vock • 0
1
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1
reply
768
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 12 months ago by ★ 3.6k • written 13 months ago by • 0
7
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28
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7.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 13 months ago by 52k • written 10.0 years ago by ★ 7.9k
0
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4
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1.0k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 13 months ago by 52k • written 13 months ago by • 0
4
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6
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1.2k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
13 months ago isaac.vock • 0
0
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2
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4.3k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.6 years ago by ▴ 80
0
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0
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1.7k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
18 months ago Gordon Smyth 52k
0
votes
2
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1.9k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 19 months ago by 68k • written 19 months ago by • 0
1
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1
reply
1.0k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 19 months ago by ▴ 450 • written 19 months ago by • 0
0
votes
1
reply
1.3k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 22 months ago by ★ 3.6k • written 22 months ago by • 0
0
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0
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669
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
23 months ago barrypraveen • 0
2
votes
9
replies
2.5k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
24 months ago Hilary ▴ 40
0
votes
2
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1.2k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.0 years ago by ★ 3.6k • written 2.3 years ago by • 0
0
votes
0
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942
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
2.0 years ago yao hua • 0
0
votes
1
reply
1.2k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.1 years ago by ▴ 450 • written 2.1 years ago by • 0
0
votes
1
reply
906
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 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
3
votes
3
replies
5.4k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
0
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1
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3.3k
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
1
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1
reply
3.1k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
0
votes
0
replies
828
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 2.3 years ago by ★ 4.7k • written 2.3 years ago by • 0
2
votes
3
replies
1.9k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
2
votes
2
replies
1.1k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
2.4 years ago dario.beraldi • 0
0
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0
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749
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.4 years ago rridley3 • 0
0
votes
2
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2.1k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
2.5 years ago KMS ▴ 20
0
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1
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4.6k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
0
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1
reply
1.0k
views
fetaure counts err
featurecounts
updated 2.6 years ago by ★ 3.6k • written 2.7 years ago by • 0
0
votes
1
reply
1.2k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.8 years ago NIK • 0
1
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1
reply
1.8k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
2
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1
reply
2.0k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.8 years ago by ★ 1.4k • written 2.8 years ago by ▴ 10
0
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4
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2.3k
views
featureCounts: 0% successfully assigned fragments
featureCounts
2.8 years ago KMS ▴ 20
1
vote
4
replies
2.1k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.8 years ago Chise ▴ 10
3
votes
11
replies
4.9k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.9 years ago • updated 2.8 years ago Sarah_piggy ▴ 10
1
vote
4
replies
2.4k
views
Subread installation
subread featureCounts
2.9 years ago Lucy ▴ 60
1
vote
5
replies
2.8k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.1 years ago • updated 3.0 years ago Lucy ▴ 60
2
votes
2
replies
7.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.2 years ago Chise ▴ 10
4
votes
4
replies
6.1k
views
FeatureCounts
counts subread RNASeq featurecounts
3.3 years ago k___ ▴ 30
0
votes
2
replies
1.9k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 2.4 years ago by • 0 • written 3.5 years ago by • 0
1
vote
1
reply
1.6k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 3.6 years ago by ★ 3.6k • written 3.6 years ago by • 0
1
vote
5
replies
6.5k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 19 months ago by ▴ 450 • written 3.7 years ago by ▴ 10
4
votes
5
replies
2.7k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
3.7 years ago • updated 3.6 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
2.3k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 4.0 years ago by ▴ 450 • written 4.0 years ago by • 0
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
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A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
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