Showing : featureCounts • reset
0
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302
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Blank gene_id in featureCounts
featureCounts Rsubread
7 months ago Meg • 0
5
votes
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
votes
1
reply
975
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 10 months ago by 53k • written 10 months ago by ▴ 80
0
votes
1
reply
892
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 12 months ago by 53k • written 21 months ago by • 0
1
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3
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1.9k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
14 months ago yasmin.hilliam ▴ 10
0
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1
reply
664
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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
votes
5
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4.2k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 11 months ago by ▴ 20 • written 16 months ago by • 0
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
17 months ago • updated 16 months ago Jessica • 0
1
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2
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940
views
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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2.0k
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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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1.2k
views
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
votes
28
replies
8.6k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 22 months ago by 53k • written 10.8 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 23 months ago by • 0
4
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6
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1.7k
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[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
23 months ago • updated 22 months ago isaac.vock • 0
0
votes
2
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5.0k
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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 2.4 years ago by 68k • written 2.4 years ago by • 0
1
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1
reply
1.3k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.4 years ago by ▴ 450 • written 2.4 years ago by • 0
0
votes
1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.6 years ago by ★ 3.6k • written 2.7 years ago by • 0
0
votes
0
replies
829
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
votes
9
replies
3.4k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.8 years ago Hilary ▴ 40
0
votes
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 3.1 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
2.8 years ago yao hua • 0
0
votes
1
reply
1.5k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.9 years ago by ▴ 450 • written 2.9 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 2.9 years ago by ★ 1.4k • written 2.9 years ago by • 0
3
votes
3
replies
7.0k
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
votes
1
reply
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 3.1 years ago by 53k • written 3.1 years ago by • 0
0
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0
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1.0k
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 3.1 years ago by ★ 5.0k • written 3.1 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
3.2 years ago dario.beraldi • 0
0
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0
replies
996
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.2 years ago rridley3 • 0
0
votes
2
replies
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 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
1.3k
views
fetaure counts err
featurecounts
updated 3.4 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
3.6 years ago NIK • 0
1
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1
reply
2.2k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.6 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
3.7 years ago • updated 3.6 years ago Sarah_piggy ▴ 10
1
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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
3.9 years ago • updated 3.8 years ago Lucy ▴ 60
2
votes
2
replies
8.6k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
4.0 years ago Chise ▴ 10
4
votes
4
replies
6.8k
views
FeatureCounts
counts subread RNASeq featurecounts
4.1 years ago k___ ▴ 30
0
votes
2
replies
2.2k
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
1.9k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 4.4 years ago by ★ 3.6k • written 4.4 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 4.5 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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Answer: segfault in edgeR glmQLFit by Gordon Smyth 53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. We will …
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
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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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