Showing : FeatureCounts • reset
0
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288
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Blank gene_id in featureCounts
featureCounts Rsubread
6 months ago Meg • 0
5
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10
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2.6k
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Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 12 months ago by • 0
0
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1
reply
956
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 9 months ago by 53k • written 9 months ago by ▴ 80
0
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1
reply
873
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 11 months ago by 53k • written 21 months ago by • 0
1
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3
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1.8k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
14 months ago • updated 13 months ago yasmin.hilliam ▴ 10
0
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1
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640
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[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
14 months ago isaac.vock • 0
6
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5
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4.1k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 11 months ago by ▴ 20 • written 15 months ago by • 0
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4
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1.2k
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
16 months ago Jessica • 0
1
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2
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914
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
16 months ago Anke • 0
4
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2
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1.9k
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
18 months ago Rachael • 0
2
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4
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1.6k
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
20 months ago • updated 18 months ago isaac.vock • 0
1
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1
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1.1k
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 21 months ago by ★ 3.6k • written 22 months ago by • 0
7
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28
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8.6k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 22 months ago by 53k • written 10.7 years ago by ★ 7.9k
0
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4
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1.5k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 22 months ago by 53k • written 22 months ago by • 0
4
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6
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1.7k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
22 months ago isaac.vock • 0
0
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2
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4.9k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.4 years ago by ▴ 80
0
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0
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2.1k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.3 years ago Gordon Smyth 53k
0
votes
2
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2.5k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
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1
reply
1.2k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.4 years ago by ▴ 450 • written 2.4 years ago by • 0
0
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1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.6 years ago by ★ 3.6k • written 2.6 years ago by • 0
0
votes
0
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819
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.7 years ago barrypraveen • 0
2
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9
replies
3.4k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.8 years ago • updated 2.7 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 2.8 years ago by ★ 3.6k • written 3.0 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
2.8 years ago yao hua • 0
0
votes
1
reply
1.5k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.8 years ago by ▴ 450 • written 2.8 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 2.8 years ago by ★ 1.4k • written 2.8 years ago by • 0
3
votes
3
replies
6.9k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
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1
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3.9k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
1
vote
1
reply
3.8k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
0
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1000
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
votes
3
replies
2.4k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
2
votes
2
replies
1.3k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
3.1 years ago dario.beraldi • 0
0
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0
replies
982
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.1 years ago rridley3 • 0
0
votes
2
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2.6k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.3 years ago • updated 3.2 years ago KMS ▴ 20
0
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1
reply
5.3k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
0
votes
1
reply
1.2k
views
fetaure counts err
featurecounts
updated 3.4 years ago by ★ 3.6k • written 3.4 years ago by • 0
0
votes
1
reply
1.4k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.5 years ago NIK • 0
1
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1
reply
2.2k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.5 years ago by 53k • written 3.6 years ago by • 0
2
votes
1
reply
2.3k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by ▴ 10
0
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4
replies
2.6k
views
featureCounts: 0% successfully assigned fragments
featureCounts
3.6 years ago KMS ▴ 20
1
vote
4
replies
2.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.6 years ago Chise ▴ 10
3
votes
11
replies
5.7k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.6 years ago Sarah_piggy ▴ 10
1
vote
4
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3.0k
views
Subread installation
subread featureCounts
3.7 years ago Lucy ▴ 60
1
vote
5
replies
3.4k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.8 years ago Lucy ▴ 60
2
votes
2
replies
8.5k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.9 years ago Chise ▴ 10
4
votes
4
replies
6.7k
views
FeatureCounts
counts subread RNASeq featurecounts
4.1 years ago k___ ▴ 30
0
votes
2
replies
2.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.2 years ago by • 0 • written 4.3 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 4.3 years ago by ★ 3.6k • written 4.3 years ago by • 0
1
vote
5
replies
7.4k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 2.4 years ago by ▴ 450 • written 4.4 years ago by ▴ 10
4
votes
5
replies
3.1k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
4.5 years ago • updated 4.4 years ago Konstantinos Yeles ▴ 90
136 results • Page 1 of 3
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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