Showing : featurecounts • reset
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
24 days ago • updated 21 days ago Gordon Smyth 48k
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2
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207
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 6 weeks ago by 63k • written 6 weeks ago by • 0
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1
reply
262
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featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 weeks ago by ▴ 380 • written 9 weeks ago by • 0
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1
reply
332
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Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 4 months ago by ★ 3.5k • written 4 months ago by • 0
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202
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
5 months ago barrypraveen • 0
2
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9
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833
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featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
6 months ago Hilary ▴ 30
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2
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492
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 6 months ago by ★ 3.5k • written 9 months ago by • 0
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253
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Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
7 months ago yao hua • 0
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1
reply
402
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Subread installation on Linux ARM64
subread featureCounts
updated 7 months ago by ▴ 380 • written 7 months ago by • 0
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1
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278
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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 7 months ago by ★ 1.3k • written 7 months ago by • 0
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3
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1.3k
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 8 months ago by 48k • written 8 months ago by • 0
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1
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995
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 9 months ago by ★ 1.3k • written 9 months ago by • 0
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1.0k
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Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 10 months ago by 48k • written 10 months ago by • 0
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300
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Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 10 months ago by ★ 3.4k • written 10 months ago by • 0
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3
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652
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Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 10 months ago by 48k • written 10 months ago by • 0
2
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2
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445
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featureCounts: No effect of setting -d and -D?
subread featureCounts
11 months ago dario.beraldi • 0
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302
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
11 months ago rridley3 • 0
0
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2
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903
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
12 months ago KMS ▴ 10
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1
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2.0k
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gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 14 months ago by 48k • written 14 months ago by • 0
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reply
502
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fetaure counts err
featurecounts
updated 14 months ago by ★ 3.5k • written 14 months ago by • 0
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1
reply
537
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
16 months ago • updated 15 months ago NIK • 0
1
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1
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1.0k
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Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 16 months ago by 48k • written 16 months ago by • 0
2
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1
reply
1.1k
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 10
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4
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1.2k
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featureCounts: 0% successfully assigned fragments
featureCounts
16 months ago KMS ▴ 10
1
vote
4
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945
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Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
17 months ago • updated 16 months ago Chise ▴ 10
3
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11
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2.6k
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The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
17 months ago • updated 16 months ago Sarah_piggy ▴ 10
1
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4
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1.1k
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Subread installation
subread featureCounts
17 months ago Lucy ▴ 60
1
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5
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1.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
19 months ago Lucy ▴ 60
2
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2
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4.2k
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"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
21 months ago Chise ▴ 10
4
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4
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3.6k
views
FeatureCounts
counts subread RNASeq featurecounts
22 months ago k___ ▴ 20
0
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2
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1.1k
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featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 11 months ago by • 0 • written 2.1 years ago by • 0
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1
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839
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Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 2.1 years ago by ★ 3.5k • written 2.1 years ago by • 0
1
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5
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3.5k
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featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 8 weeks ago by ▴ 380 • written 2.2 years ago by ▴ 10
4
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5
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1.6k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.3 years ago • updated 2.2 years ago Konstantinos Yeles ▴ 80
2
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2
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1.4k
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Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 2.6 years ago by ▴ 380 • written 2.6 years ago by • 0
6
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26
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4.8k
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Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.8 years ago by ▴ 380 • written 8.5 years ago by 7.8k
0
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0
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543
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Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
2.9 years ago martinag.work • 0
0
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1
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2.8k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
updated 3.2 years ago by ★ 1.3k • written 3.2 years ago by ▴ 80
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2
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2.9k
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
3.5 years ago chatterjee.arumoy ▴ 10
2
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3
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1.6k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 3.8 years ago by 63k • written 3.8 years ago by • 0
4
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2
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924
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.0 years ago by ★ 1.3k • written 4.0 years ago by • 0
0
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2
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814
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Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.1 years ago by ★ 3.5k • written 4.1 years ago by • 0
4
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3
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3.8k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.2 years ago by ★ 3.5k • written 4.2 years ago by ▴ 80
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2
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2.1k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 4.2 years ago by 48k • written 4.2 years ago by • 0
1
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1
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700
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featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 40
5
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11
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3.2k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 17 months ago by ▴ 10 • written 4.4 years ago by ▴ 120
3
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7
replies
1.6k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
1
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1
reply
2.4k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 4.5 years ago by ★ 3.5k • written 4.5 years ago by ▴ 10
7
votes
5
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3.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 4.5 years ago by 48k • written 4.5 years ago by ▴ 60
2
votes
6
replies
1.5k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 4.5 years ago by ★ 3.5k • written 4.5 years ago by • 0
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Comment: List of Deprecated Packages for Bioc3.18 by Hervé Pagès 16k
Also the source package is not available [in BioC 3.17](https://bioconductor.org/packages/3.17/CancerInSilico) which means that the package…
Answer: DelayedArray::read_sparse_block by Hervé Pagès 16k
Hi Koki, Sorry again for the slow response. `read_sparse_block()` has been around for years. It's a generic function defined in the *…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Votes
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
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