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Showing :
FeatureCounts
•
reset
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
25 days ago • updated 6 days ago
isaac.vock
• 0
0
votes
0
replies
133
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
7 weeks ago
chris2.a.white
• 0
1
vote
1
reply
247
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 7 weeks ago by
Wei Shi
★ 3.6k • written 11 weeks ago by
Alex
• 0
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 11 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
4
replies
418
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
tjgray4
• 0
4
votes
6
replies
736
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago • updated 12 weeks ago
isaac.vock
• 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
0
votes
0
replies
927
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
8 months ago • updated 7 months ago
Gordon Smyth
50k
0
votes
2
replies
1.0k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
vitoriastavis
• 0
1
vote
1
reply
651
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 9 months ago by
StevenE.Strong
• 0
0
votes
1
reply
854
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 11 months ago by
Wei Shi
★ 3.6k • written 12 months ago by
Carlos
• 0
0
votes
0
replies
417
views
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
votes
9
replies
1.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0
featureCounts
T2T
Rsubread
13 months ago
Hilary
▴ 30
0
votes
2
replies
850
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread
featureCounts
updated 14 months ago by
Wei Shi
★ 3.6k • written 17 months ago by
Konstantin
• 0
0
votes
0
replies
616
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
14 months ago
yao hua
• 0
0
votes
1
reply
769
views
Subread installation on Linux ARM64
subread
featureCounts
updated 14 months ago by
Yang Liao
▴ 380 • written 15 months ago by
Keyu
• 0
0
votes
1
reply
547
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 15 months ago by
swbarnes2
★ 1.3k • written 15 months ago by
Bo
• 0
3
votes
3
replies
2.7k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Sara
• 0
0
votes
1
reply
1.9k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads
STAR
featureCounts
updated 16 months ago by
swbarnes2
★ 1.3k • written 16 months ago by
lalala
• 0
1
vote
1
reply
1.9k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Sara
• 0
0
votes
0
replies
573
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 17 months ago by
ATpoint
★ 4.0k • written 17 months ago by
Leon
• 0
2
votes
3
replies
1.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Jon
• 0
2
votes
2
replies
762
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
18 months ago
dario.beraldi
• 0
0
votes
0
replies
524
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
18 months ago
rridley3
• 0
0
votes
2
replies
1.4k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
19 months ago
KMS
▴ 20
0
votes
1
reply
3.2k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
selmanurkeskin
• 0
0
votes
1
reply
728
views
fetaure counts err
featurecounts
updated 21 months ago by
Wei Shi
★ 3.6k • written 22 months ago by
哲
• 0
0
votes
1
reply
827
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
23 months ago
NIK
• 0
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
margo
• 0
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 23 months ago by
swbarnes2
★ 1.3k • written 23 months ago by
Hicham
▴ 10
0
votes
4
replies
1.7k
views
featureCounts: 0% successfully assigned fragments
featureCounts
23 months ago
KMS
▴ 20
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
24 months ago
Chise
▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.0 years ago • updated 24 months ago
Sarah_piggy
▴ 10
1
vote
4
replies
1.6k
views
Subread installation
subread
featureCounts
2.0 years ago
Lucy
▴ 60
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.2 years ago
Lucy
▴ 60
2
votes
2
replies
5.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts
Rsubread
2.3 years ago
Chise
▴ 10
4
votes
4
replies
4.9k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
0
votes
2
replies
1.4k
views
featureCounts: unable to find chromosome in SAM header
RNASeq
featureCounts
updated 18 months ago by
marie
• 0 • written 2.7 years ago by
nklier38
• 0
1
vote
1
reply
1.2k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.7 years ago by
Wei Shi
★ 3.6k • written 2.7 years ago by
dario.beraldi
• 0
1
vote
5
replies
4.7k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 2.8 years ago by
s.muroy
▴ 10
4
votes
5
replies
2.1k
views
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
votes
2
replies
1.8k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.1 years ago by
Yang Liao
▴ 380 • written 3.1 years ago by
Jason
• 0
0
votes
0
replies
767
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread
featureCounts
3.5 years ago
martinag.work
• 0
1
vote
2
replies
3.5k
views
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
votes
3
replies
1.9k
views
RNAseq read counts generated by FeatureCounts
featurecounts
RNAseq
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
adeler001
• 0
4
votes
2
replies
1.2k
views
bwa mem to feature Counts
bwa mem
featureCounts
updated 4.6 years ago by
swbarnes2
★ 1.3k • written 4.6 years ago by
ajajoo
• 0
0
votes
2
replies
1.0k
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 4.7 years ago by
Wei Shi
★ 3.6k • written 4.7 years ago by
hafiz.talhamalik
• 0
4
votes
3
replies
4.3k
views
Rsubread, Error in featureCounts paired end
Rsubread
paired end
featureCounts
updated 4.8 years ago by
Wei Shi
★ 3.6k • written 4.8 years ago by
hauken_heyken
▴ 80
1
vote
2
replies
2.7k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 4.8 years ago by
Gordon Smyth
50k • written 4.8 years ago by
algenubi81
• 0
1
vote
1
reply
878
views
featureCounts Does Not Correctly Parse File Names
Rsubread
featureCounts
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
wunderl
▴ 40
50 results • Page
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
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That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
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▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
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★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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