Showing : FeatureCounts • reset
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
updated 9 days ago by ★ 3.6k • written 18 days ago by • 0
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124
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Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
6 weeks ago chris2.a.white • 0
1
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1
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236
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 6 weeks ago by ★ 3.6k • written 10 weeks ago by • 0
7
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28
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6.1k
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Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 10 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
0
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4
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404
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Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
4
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6
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723
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[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
11 weeks ago isaac.vock • 0
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2
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3.5k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.7 years ago by ▴ 80
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903
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
7 months ago Gordon Smyth 50k
0
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2
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981
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
1
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1
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639
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featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
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1
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839
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Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 11 months ago by ★ 3.6k • written 11 months ago by • 0
0
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0
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406
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
12 months ago barrypraveen • 0
2
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9
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1.6k
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featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
13 months ago Hilary ▴ 30
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2
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836
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 13 months ago by ★ 3.6k • written 16 months ago by • 0
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607
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Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
14 months ago yao hua • 0
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1
reply
747
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Subread installation on Linux ARM64
subread featureCounts
updated 14 months ago by ▴ 380 • written 14 months ago by • 0
0
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1
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528
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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 14 months ago by ★ 1.3k • written 14 months ago by • 0
3
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3
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2.6k
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 15 months ago by 50k • written 15 months ago by • 0
0
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1
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1.9k
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 16 months ago by ★ 1.3k • written 16 months ago by • 0
1
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1
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1.8k
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Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 16 months ago by 50k • written 17 months ago by • 0
0
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564
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Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
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3
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1.2k
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Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 17 months ago by 50k • written 17 months ago by • 0
2
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2
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748
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featureCounts: No effect of setting -d and -D?
subread featureCounts
18 months ago dario.beraldi • 0
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0
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513
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
18 months ago rridley3 • 0
0
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2
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1.4k
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
19 months ago KMS ▴ 20
0
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1
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3.2k
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gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 21 months ago by 50k • written 21 months ago by • 0
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1
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713
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fetaure counts err
featurecounts
updated 21 months ago by ★ 3.6k • written 21 months ago by • 0
0
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1
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817
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
23 months ago • updated 22 months ago NIK • 0
1
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1
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1.4k
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Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 23 months ago by 50k • written 23 months ago by • 0
2
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1
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1.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by ▴ 10
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4
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1.7k
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featureCounts: 0% successfully assigned fragments
featureCounts
23 months ago KMS ▴ 20
1
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4
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1.4k
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Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
24 months ago • updated 23 months ago Chise ▴ 10
3
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11
replies
3.5k
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The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago • updated 23 months ago Sarah_piggy ▴ 10
1
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4
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1.5k
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Subread installation
subread featureCounts
2.0 years ago Lucy ▴ 60
1
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5
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1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
2
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2
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5.8k
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"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.3 years ago Chise ▴ 10
4
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4
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4.8k
views
FeatureCounts
counts subread RNASeq featurecounts
2.4 years ago k___ ▴ 30
0
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2
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1.4k
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featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 18 months ago by • 0 • written 2.6 years ago by • 0
1
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1
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1.1k
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Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.7 years ago by • 0
1
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5
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4.6k
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featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 8 months ago by ▴ 380 • written 2.8 years ago by ▴ 10
4
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5
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2.1k
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Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.9 years ago • updated 2.8 years ago Konstantinos Yeles ▴ 80
2
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2
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1.8k
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Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.1 years ago by ▴ 380 • written 3.1 years ago by • 0
0
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0
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756
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Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
3.5 years ago martinag.work • 0
1
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2
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3.5k
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.1 years ago chatterjee.arumoy ▴ 10
2
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3
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1.9k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
4
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2
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1.2k
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by • 0
0
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2
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1.0k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.7 years ago by ★ 3.6k • written 4.7 years ago by • 0
4
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3
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4.3k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.8 years ago by ★ 3.6k • written 4.8 years ago by ▴ 80
1
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2
replies
2.7k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 4.8 years ago by 50k • written 4.8 years ago by • 0
1
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1
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867
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 40
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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