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Showing :
featureCounts
•
reset
2
votes
2
replies
2.5k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 4.6 years ago by
Yang Liao
▴ 450 • written 4.6 years ago by
Jason
• 0
0
votes
0
replies
1.1k
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread
featureCounts
5.0 years ago
martinag.work
• 0
1
vote
2
replies
4.7k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
5.6 years ago
chatterjee.arumoy
▴ 10
2
votes
3
replies
2.4k
views
RNAseq read counts generated by FeatureCounts
featurecounts
RNAseq
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
adeler001
• 0
4
votes
2
replies
1.8k
views
bwa mem to feature Counts
bwa mem
featureCounts
updated 6.1 years ago by
swbarnes2
★ 1.4k • written 6.1 years ago by
ajajoo
• 0
0
votes
2
replies
1.4k
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 6.2 years ago by
Wei Shi
★ 3.6k • written 6.2 years ago by
hafiz.talhamalik
• 0
4
votes
3
replies
5.4k
views
Rsubread, Error in featureCounts paired end
Rsubread
paired end
featureCounts
updated 6.3 years ago by
Wei Shi
★ 3.6k • written 6.3 years ago by
hauken_heyken
▴ 80
1
vote
2
replies
3.8k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 6.3 years ago by
Gordon Smyth
53k • written 6.3 years ago by
algenubi81
• 0
1
vote
1
reply
1.1k
views
featureCounts Does Not Correctly Parse File Names
Rsubread
featureCounts
updated 6.4 years ago by
Gordon Smyth
53k • written 6.4 years ago by
wunderl
▴ 40
5
votes
11
replies
5.4k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread
featureCounts
updated 3.5 years ago by
Sarah_piggy
▴ 10 • written 6.5 years ago by
k.vitting.seerup
▴ 120
3
votes
7
replies
2.6k
views
Rsubread inbuilt annotation
rsubread
featureCounts
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
diego.carvalhoalvarez
• 0
1
vote
1
reply
4.1k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 6.5 years ago by
Wei Shi
★ 3.6k • written 6.5 years ago by
aurel.nagy
▴ 10
7
votes
5
replies
5.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts
rnaseq
Rsubread
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
Raito92
▴ 60
2
votes
6
replies
2.7k
views
featurecounts Rsubread ERROR on exon_id
R
error
software error
Rsubread
featurecounts
updated 6.6 years ago by
Wei Shi
★ 3.6k • written 6.6 years ago by
edejong
• 0
1
vote
2
replies
2.1k
views
Problem with importing text file in featureCounts
Rsubread
featureCounts
updated 6.6 years ago by
Gordon Smyth
53k • written 6.6 years ago by
estevemp
• 0
3
votes
2
replies
2.9k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq
featureCounts
STAR
minMQS
mapping quality score
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
Gary
▴ 20
0
votes
5
replies
2.9k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
leo_CD
• 0
3
votes
13
replies
4.0k
views
Rsubread- feature counts
annotation
Rsubread
featureCounts
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
memoly101
• 0
1
vote
3
replies
1.8k
views
how to find expressed genes in RNAseq
deseq2
rnaseq
differential gene expression
featurecounts
rnaseqGene
6.8 years ago
melkile26
• 0
0
votes
9
replies
4.0k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts
Rsubread
ggbio
updated 6.9 years ago by
Wei Shi
★ 3.6k • written 6.9 years ago by
A
▴ 60
1
vote
1
reply
3.0k
views
Warning using feuture count related to GTF file
featurecounts
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
roghaiyeh.safari
• 0
0
votes
1
reply
1.3k
views
weired output with featurecount
featurecounts
star
7.1 years ago
roghaiyeh.safari
• 0
0
votes
6
replies
2.2k
views
Options Request for FeatureCounts
featurecounts
subread
updated 7.2 years ago by
Wei Shi
★ 3.6k • written 7.2 years ago by
Leon
• 0
0
votes
6
replies
4.1k
views
Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
deseq2
featurecounts
error message
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Yuqia
• 0
4
votes
5
replies
2.0k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
rogangrant
• 0
3
votes
2
replies
3.7k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 7.3 years ago by
Gordon Smyth
53k • written 7.3 years ago by
JennyS
• 0
4
votes
2
replies
6.0k
views
featureCounts for multiple features
featurecounts
updated 2.9 years ago by
hermidalc
▴ 20 • written 7.3 years ago by
hwu12
▴ 10
1
vote
2
replies
2.2k
views
How to change sample names in featureCounts or edgeR
featurecounts
edgeR
updated 7.4 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Gary
▴ 20
2
votes
3
replies
1.8k
views
How edgeR reads an R List object produced by featureCounts
edger
featurecounts
updated 2.6 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Gary
▴ 20
0
votes
8
replies
4.6k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread
featurecounts
7.4 years ago
connor.geraghty
• 0
0
votes
2
replies
4.1k
views
lncRNA annotation for featureCouns and STAR
lncRNA
featureCounts
STAR
annotation
updated 7.4 years ago by
Wei Shi
★ 3.6k • written 7.4 years ago by
inah
▴ 10
4
votes
7
replies
3.5k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq
deseq2
featurecounts
differential binding analysis
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
hkarakurt
▴ 20
6
votes
6
replies
7.9k
views
strange results with featureCounts
RNA-seq
featureCounts
total RNA
updated 3.0 years ago by
snijesh
▴ 200 • written 7.4 years ago by
inah
▴ 10
0
votes
4
replies
4.4k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts
r
rnaseq
7.5 years ago
octopuslegs11
• 0
1
vote
4
replies
2.0k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq
rsubread
featurecounts
updated 7.7 years ago by
Wei Shi
★ 3.6k • written 7.7 years ago by
mmurshed
• 0
0
votes
1
reply
1.5k
views
featureCounts : limits on multioverlap (option -O)
featurecounts
read counting
updated 7.7 years ago by
Gordon Smyth
53k • written 7.7 years ago by
marc.gabriel.01
• 0
0
votes
1
reply
1.7k
views
Rsubread Read Bam and filter reads by TAG field
Rsubread
featurecounts
featurerequest
7.8 years ago
alessandro.pastore
▴ 20
0
votes
7
replies
3.0k
views
caught segfault when using featureCounts
rsubread
featurecounts
7.9 years ago • updated 7.8 years ago
Ge Tan
▴ 20
4
votes
15
replies
5.4k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2
rnaseq
featurecounts
DESeqDataSetFromMatrix
updated 7.9 years ago by
Michael Love
43k • written 8.0 years ago by
bioinf
▴ 10
5
votes
3
replies
6.8k
views
Rsubread counting peaks ATACseq
Rsubread
atac-seq
narrowpeaks
featurecounts
updated 7.9 years ago by
Wei Shi
★ 3.6k • written 7.9 years ago by
j.bergenstrahle
▴ 90
3
votes
1
reply
3.0k
views
Explainnation of featureCounts in-built annotation?
rnaseq
annotation
featurecounts
updated 8.0 years ago by
Wei Shi
★ 3.6k • written 8.0 years ago by
Jack
▴ 20
3
votes
1
reply
1.6k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq
annotation
featurecounts
biomart
updated 8.0 years ago by
James W. MacDonald
68k • written 8.0 years ago by
Jack
▴ 20
4
votes
8
replies
2.2k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq
featurecounts
edger
deseq2
updated 8.0 years ago by
Gordon Smyth
53k • written 8.0 years ago by
Jack
▴ 20
0
votes
1
reply
920
views
Feature Count annotation file problem
annotation
featurecounts
8.1 years ago
fatemeh.kaveh
• 0
0
votes
6
replies
2.6k
views
Rsubread featureCounts with byReadGroup
rsubread
featurecounts
updated 8.1 years ago by
Yang Liao
▴ 450 • written 8.1 years ago by
Ge Tan
▴ 20
1
vote
1
reply
2.4k
views
featureCounts using 3'UTR as genome
featurecounts
R
updated 8.2 years ago by
James W. MacDonald
68k • written 8.2 years ago by
joangibert14
• 0
2
votes
14
replies
9.6k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 2.7 years ago by
Chris
▴ 20 • written 8.2 years ago by
Biologist
▴ 120
1
vote
5
replies
4.0k
views
using paired end and single end data in featurecounts
featurecounts
rsubread
updated 8.2 years ago by
James W. MacDonald
68k • written 8.2 years ago by
nikelle.petrillo
• 0
0
votes
3
replies
3.2k
views
featureCount and bam
featurecounts
8.3 years ago
Morris
▴ 10
0
votes
3
replies
3.4k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread
featurecounts
exon
mRNAseq
updated 8.4 years ago by
Wei Shi
★ 3.6k • written 8.4 years ago by
inah
▴ 10
136 results • Page
2 of 3
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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