Showing : featurecounts • reset
6
votes
3
replies
835
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 25 days ago by 67k • written 26 days ago by • 0
0
votes
4
replies
546
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
8 weeks ago • updated 5 weeks ago Jessica • 0
1
vote
2
replies
384
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
6 weeks ago • updated 5 weeks ago Anke • 0
4
votes
2
replies
415
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
3 months ago Rachael • 0
2
votes
4
replies
796
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
5 months ago • updated 3 months ago isaac.vock • 0
0
votes
0
replies
294
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
6 months ago chris2.a.white • 0
1
vote
1
reply
508
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 6 months ago by ★ 3.6k • written 7 months ago by • 0
7
votes
28
replies
6.7k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 7 months ago by 51k • written 9.5 years ago by ★ 7.9k
0
votes
4
replies
699
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 7 months ago by 51k • written 7 months ago by • 0
4
votes
6
replies
972
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
7 months ago isaac.vock • 0
0
votes
2
replies
3.9k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.2 years ago by ▴ 80
0
votes
0
replies
1.3k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
12 months ago Gordon Smyth 51k
0
votes
2
replies
1.4k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 13 months ago by 67k • written 13 months ago by • 0
1
vote
1
reply
829
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 14 months ago by ▴ 440 • written 14 months ago by • 0
0
votes
1
reply
1.1k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 16 months ago by ★ 3.6k • written 16 months ago by • 0
0
votes
0
replies
543
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
17 months ago barrypraveen • 0
2
votes
9
replies
2.1k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
18 months ago Hilary ▴ 40
0
votes
2
replies
1.1k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 18 months ago by ★ 3.6k • written 21 months ago by • 0
0
votes
0
replies
770
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
19 months ago yao hua • 0
0
votes
1
reply
974
views
Subread installation on Linux ARM64
subread featureCounts
updated 19 months ago by ▴ 440 • written 19 months ago by • 0
0
votes
1
reply
751
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 19 months ago by ★ 1.4k • written 19 months ago by • 0
3
votes
3
replies
3.7k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 20 months ago by 51k • written 20 months ago by • 0
0
votes
1
reply
2.5k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 21 months ago by ★ 1.4k • written 21 months ago by • 0
1
vote
1
reply
2.4k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 21 months ago by 51k • written 22 months ago by • 0
0
votes
0
replies
681
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 22 months ago by ★ 4.4k • written 22 months ago by • 0
2
votes
3
replies
1.5k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 22 months ago by 51k • written 22 months ago by • 0
2
votes
2
replies
928
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
23 months ago dario.beraldi • 0
0
votes
0
replies
632
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
23 months ago rridley3 • 0
0
votes
2
replies
1.7k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
2.0 years ago KMS ▴ 20
0
votes
1
reply
3.9k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
votes
1
reply
911
views
fetaure counts err
featurecounts
updated 2.1 years ago by ★ 3.6k • written 2.2 years ago by • 0
0
votes
1
reply
1.0k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.3 years ago NIK • 0
1
vote
1
reply
1.6k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.3 years ago by 51k • written 2.3 years ago by • 0
2
votes
1
reply
1.7k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by ▴ 10
0
votes
4
replies
2.0k
views
featureCounts: 0% successfully assigned fragments
featureCounts
2.3 years ago KMS ▴ 20
1
vote
4
replies
1.7k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.4 years ago Chise ▴ 10
3
votes
11
replies
4.2k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.4 years ago Sarah_piggy ▴ 10
1
vote
4
replies
2.0k
views
Subread installation
subread featureCounts
2.4 years ago Lucy ▴ 60
1
vote
5
replies
2.4k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.6 years ago Lucy ▴ 60
2
votes
2
replies
6.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.7 years ago Chise ▴ 10
4
votes
4
replies
5.5k
views
FeatureCounts
counts subread RNASeq featurecounts
2.8 years ago k___ ▴ 30
0
votes
2
replies
1.6k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 23 months ago by • 0 • written 3.1 years ago by • 0
1
vote
1
reply
1.3k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 3.1 years ago by ★ 3.6k • written 3.1 years ago by • 0
1
vote
5
replies
5.4k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 13 months ago by ▴ 440 • written 3.2 years ago by ▴ 10
4
votes
5
replies
2.4k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
3.3 years ago • updated 3.2 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
2.1k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.5 years ago by ▴ 440 • written 3.5 years ago by • 0
0
votes
0
replies
880
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
3.9 years ago martinag.work • 0
1
vote
2
replies
3.9k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.5 years ago chatterjee.arumoy ▴ 10
2
votes
3
replies
2.1k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 4.8 years ago by 67k • written 4.8 years ago by • 0
4
votes
2
replies
1.4k
views
bwa mem to feature Counts
bwa mem featureCounts
updated 5.0 years ago by ★ 1.4k • written 5.0 years ago by • 0
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Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
The odds ratio, not log FC. My bad.
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
``` testResult$Eff_Condition > 0.1 ```
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Hello, Thank you. I absolutely respect what you mention about p-values and logFC, I was just going to tackle that soon and thank you for po…
Comment: QSEA:Error in h(simpleError(msg, call)) by kf • 0
genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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