Showing : FeatureCounts • reset
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36
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Subread installation on Linux ARM64
subread featureCounts
3 days ago Keyu • 0
0
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1
reply
49
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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 4 days ago by ★ 1.2k • written 4 days ago by • 0
3
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3
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166
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 23 days ago by 47k • written 23 days ago by • 0
0
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1
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208
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 8 weeks ago by ★ 1.2k • written 8 weeks ago by • 0
0
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1
reply
158
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 5 days ago by ★ 3.5k • written 9 weeks ago by • 0
1
vote
1
reply
184
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 10 weeks ago by 47k • written 10 weeks ago by • 0
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0
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83
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Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 11 weeks ago by ★ 2.1k • written 11 weeks ago by • 0
2
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3
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191
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Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 12 weeks ago by 47k • written 12 weeks ago by • 0
2
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2
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177
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featureCounts: No effect of setting -d and -D?
subread featureCounts
3 months ago dario.beraldi • 0
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0
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99
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3 months ago rridley3 • 0
0
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2
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439
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
5 months ago KMS ▴ 10
0
votes
1
reply
646
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gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 6 months ago by 47k • written 6 months ago by • 0
0
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1
reply
313
views
fetaure counts err
featurecounts
updated 6 months ago by ★ 3.5k • written 7 months ago by • 0
0
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1
reply
297
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
8 months ago NIK • 0
1
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1
reply
562
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Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 8 months ago by 47k • written 8 months ago by • 0
2
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1
reply
464
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 8 months ago by ★ 1.2k • written 8 months ago by • 0
0
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4
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645
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featureCounts: 0% successfully assigned fragments
featureCounts
8 months ago KMS ▴ 10
1
vote
4
replies
499
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
9 months ago Chise ▴ 10
3
votes
11
replies
1.2k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
9 months ago Sarah_piggy ▴ 10
1
vote
4
replies
561
views
Subread installation
subread featureCounts
9 months ago Lucy ▴ 60
1
vote
5
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776
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
11 months ago Lucy ▴ 60
2
votes
2
replies
2.2k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
13 months ago Chise ▴ 10
4
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4
replies
2.0k
views
FeatureCounts
counts subread RNASeq featurecounts
15 months ago k___ ▴ 20
0
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2
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727
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featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3 months ago by • 0 • written 17 months ago by • 0
1
vote
1
reply
523
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 18 months ago by ★ 3.5k • written 18 months ago by • 0
1
vote
3
replies
2.1k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 19 months ago by ★ 3.5k • written 19 months ago by ▴ 10
4
votes
5
replies
999
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
20 months ago • updated 19 months ago Konstantinos Yeles ▴ 70
2
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2
replies
984
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 23 months ago by ▴ 350 • written 23 months ago by • 0
6
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26
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4.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.1 years ago by ▴ 350 • written 7.9 years ago by 7.8k
0
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0
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388
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
2.3 years ago martinag.work • 0
0
votes
1
reply
2.0k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
updated 2.5 years ago by ★ 1.2k • written 2.5 years ago by ▴ 50
1
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2
replies
2.0k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
2.9 years ago chatterjee.arumoy ▴ 10
2
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3
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1.1k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 3.2 years ago by 62k • written 3.2 years ago by • 0
4
votes
2
replies
673
views
bwa mem to feature Counts
bwa mem featureCounts
updated 3.3 years ago by ★ 1.2k • written 3.3 years ago by • 0
0
votes
2
replies
562
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 3.5 years ago by ★ 3.5k • written 3.5 years ago by • 0
4
votes
3
replies
3.2k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 3.6 years ago by ★ 3.5k • written 3.6 years ago by ▴ 80
1
vote
2
replies
1.4k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 3.6 years ago by 47k • written 3.6 years ago by • 0
1
vote
1
reply
508
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 3.7 years ago by 47k • written 3.7 years ago by ▴ 30
5
votes
11
replies
2.5k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 9 months ago by ▴ 10 • written 3.8 years ago by ▴ 120
3
votes
7
replies
1.2k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 3.8 years ago by 47k • written 3.8 years ago by • 0
1
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1
reply
1.9k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 3.8 years ago by ★ 3.5k • written 3.8 years ago by ▴ 10
7
votes
5
replies
2.4k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 3.8 years ago by 47k • written 3.8 years ago by ▴ 60
2
votes
6
replies
1.2k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 3.8 years ago by ★ 3.5k • written 3.8 years ago by • 0
1
vote
2
replies
813
views
Problem with importing text file in featureCounts
Rsubread featureCounts
updated 3.9 years ago by 47k • written 3.9 years ago by • 0
3
votes
2
replies
1.4k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq featureCounts STAR minMQS mapping quality score
updated 4.0 years ago by 47k • written 4.0 years ago by ▴ 20
0
votes
5
replies
1.3k
views
featureCounts error : SAM_pairer_iterate_tags
subread featureCounts
updated 4.0 years ago by 47k • written 4.0 years ago by • 0
3
votes
13
replies
1.9k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 4.0 years ago by 47k • written 4.0 years ago by • 0
1
vote
3
replies
728
views
how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
4.1 years ago melkile26 • 0
0
votes
9
replies
1.8k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 4.2 years ago by ★ 3.5k • written 4.2 years ago by ▴ 40
1
vote
1
reply
2.1k
views
Warning using feuture count related to GTF file
featurecounts
updated 4.4 years ago by 62k • written 4.4 years ago by • 0
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Comment: mas5calls function doesn't work; mirna40cdf problem by Berna • 0
Thanks for all answers. I have tried, but still get an error message. Do you know how I can work around this? > library(pd.mir…
Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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