Showing : featureCounts • reset
3
votes
4
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310
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Clarification on counting in Rsubread (featureCounts)
featureCounts Rsubread
updated 3 days ago by 53k • written 4 weeks ago by • 0
0
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0
replies
325
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Blank gene_id in featureCounts
featureCounts Rsubread
8 months ago Meg • 0
5
votes
10
replies
2.7k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 13 months ago by • 0
0
votes
1
reply
1.1k
views
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
0
votes
1
reply
941
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 13 months ago by 53k • written 22 months ago by • 0
1
vote
3
replies
2.1k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
15 months ago yasmin.hilliam ▴ 10
0
votes
1
reply
750
views
[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
votes
5
replies
4.5k
views
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
0
votes
4
replies
1.3k
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
18 months ago • updated 17 months ago Jessica • 0
1
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2
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998
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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
replies
2.3k
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
19 months ago Rachael • 0
2
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4
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1.7k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
21 months ago • updated 19 months ago isaac.vock • 0
1
vote
1
reply
1.2k
views
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
votes
28
replies
8.9k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 23 months ago by 53k • written 10.9 years ago by ★ 7.9k
0
votes
4
replies
1.6k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 23 months ago by 53k • written 23 months ago by • 0
4
votes
6
replies
1.7k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
24 months ago • updated 23 months ago isaac.vock • 0
0
votes
2
replies
5.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.5 years ago by ▴ 80
0
votes
0
replies
2.2k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.4 years ago Gordon Smyth 53k
0
votes
2
replies
2.6k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
1
reply
1.3k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.5 years ago by ▴ 450 • written 2.5 years ago by • 0
0
votes
1
reply
1.6k
views
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
votes
0
replies
855
views
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
votes
9
replies
3.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.9 years ago Hilary ▴ 40
0
votes
2
replies
1.5k
views
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
votes
0
replies
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
votes
1
reply
1.6k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.9 years ago by ▴ 450 • written 3.0 years ago by • 0
0
votes
1
reply
1.2k
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 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
3
votes
3
replies
7.1k
views
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
votes
1
reply
4.0k
views
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
vote
1
reply
4.0k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.1 years ago by 53k • written 3.2 years ago by • 0
0
votes
0
replies
1.0k
views
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
votes
3
replies
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
votes
2
replies
1.4k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
3.2 years ago dario.beraldi • 0
0
votes
0
replies
1.0k
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.3 years ago rridley3 • 0
0
votes
2
replies
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
votes
1
reply
5.4k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
1
reply
1.3k
views
fetaure counts err
featurecounts
updated 3.5 years ago by ★ 3.6k • written 3.5 years ago by • 0
0
votes
1
reply
1.5k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.7 years ago • updated 3.6 years ago NIK • 0
1
vote
1
reply
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
votes
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
votes
4
replies
2.7k
views
featureCounts: 0% successfully assigned fragments
featureCounts
3.7 years ago KMS ▴ 20
1
vote
4
replies
2.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.7 years ago Chise ▴ 10
3
votes
11
replies
5.9k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.8 years ago • updated 3.7 years ago Sarah_piggy ▴ 10
1
vote
4
replies
3.1k
views
Subread installation
subread featureCounts
3.8 years ago Lucy ▴ 60
1
vote
5
replies
3.5k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.9 years ago Lucy ▴ 60
2
votes
2
replies
8.6k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
4.1 years ago Chise ▴ 10
4
votes
4
replies
6.8k
views
FeatureCounts
counts subread RNASeq featurecounts
4.2 years ago k___ ▴ 30
0
votes
2
replies
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
vote
1
reply
1.9k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 4.5 years ago by ★ 3.6k • written 4.5 years ago by • 0
1
vote
5
replies
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
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
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It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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