Showing : FeatureCounts • reset
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538
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 14 days ago by 52k • written 15 days ago by ▴ 80
4
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8
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1.2k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
11 weeks ago • updated 10 weeks ago chris2.a.white • 0
0
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1
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565
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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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810
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
4 months ago yasmin.hilliam ▴ 10
0
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1
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326
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[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
4 months ago isaac.vock • 0
6
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5
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2.4k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 7 weeks ago by ▴ 20 • written 6 months ago by • 0
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4
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839
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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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603
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
7 months ago • updated 6 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
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756
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 12 months ago by ★ 3.6k • written 12 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
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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
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1.0k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 19 months ago by ▴ 450 • written 19 months ago by • 0
0
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1
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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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663
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
22 months ago barrypraveen • 0
2
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9
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2.5k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
24 months ago Hilary ▴ 40
0
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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 24 months ago by ★ 3.6k • written 2.2 years ago by • 0
0
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0
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933
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
2.0 years ago yao hua • 0
0
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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
901
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
5.3k
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
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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
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0
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826
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
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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
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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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744
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.4 years ago rridley3 • 0
0
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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
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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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2.2k
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
4.8k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.9 years ago • updated 2.8 years ago Sarah_piggy ▴ 10
1
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4
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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
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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
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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
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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: 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…
Answer: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
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As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
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Unbalanced experiment with multiple samples from each patient.
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