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Showing :
SubRead
•
reset
4
votes
3
replies
815
views
RSubread in cygwin
subread
4.0 years ago
Diana
▴ 10
4
votes
2
replies
737
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 3.8 years ago by
Gordon Smyth
47k • written 3.8 years ago by
Jonathan Griffiths
▴ 40
4
votes
4
replies
2.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
14 months ago
k___
▴ 20
4
votes
5
replies
856
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 4.4 years ago by
Gordon Smyth
47k • written 4.4 years ago by
rogangrant
• 0
3
votes
2
replies
2.4k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 4.6 years ago by
Gordon Smyth
47k • written 4.6 years ago by
jennyl.smith12
• 0
3
votes
3
replies
1.8k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
updated 3.4 years ago by
Wei Shi
★ 3.5k • written 3.4 years ago by
Patrick
• 0
3
votes
11
replies
1.2k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
9 months ago
Sarah_piggy
▴ 10
3
votes
2
replies
1.8k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 5.8 years ago by
Wei Shi
★ 3.5k • written 5.8 years ago by
jma1991
▴ 70
2
votes
2
replies
170
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
3 months ago
dario.beraldi
• 0
2
votes
2
replies
1.0k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 7.1 years ago by
Wei Shi
★ 3.5k • written 7.1 years ago by
Vivek.b
▴ 100
2
votes
2
replies
972
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 23 months ago by
Yang Liao
▴ 340 • written 23 months ago by
Jason
• 0
1
vote
1
reply
307
views
Threads on Subread
Slurm
Subread
updated 9 months ago by
ATpoint
★ 2.1k • written 9 months ago by
sha-ked
• 0
1
vote
1
reply
180
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 9 weeks ago by
Gordon Smyth
47k • written 10 weeks ago by
Sara
• 0
1
vote
5
replies
771
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
11 months ago
Lucy
▴ 60
1
vote
1
reply
518
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 18 months ago by
Wei Shi
★ 3.5k • written 18 months ago by
dario.beraldi
• 0
1
vote
1
reply
1.9k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 3.8 years ago by
Wei Shi
★ 3.5k • written 3.8 years ago by
aurel.nagy
▴ 10
1
vote
2
replies
1.4k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 3.6 years ago by
Gordon Smyth
47k • written 3.6 years ago by
algenubi81
• 0
1
vote
5
replies
1.2k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 2.6 years ago by
James W. MacDonald
62k • written 2.6 years ago by
abano
• 0
1
vote
3
replies
2.1k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 19 months ago by
Wei Shi
★ 3.5k • written 19 months ago by
s.muroy
▴ 10
1
vote
4
replies
550
views
Subread installation
subread
featureCounts
9 months ago
Lucy
▴ 60
0
votes
0
replies
258
views
SUBREAD Aligning reads with reference genome - Error in align The number of input file names is different from the number of output file names.
align
Alignment
subread
9 months ago
saira
• 0
0
votes
6
replies
930
views
Options Request for FeatureCounts
featurecounts
subread
updated 4.4 years ago by
Wei Shi
★ 3.5k • written 4.4 years ago by
Leon
• 0
0
votes
1
reply
493
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 3.8 years ago by
Yang Liao
▴ 340 • written 3.8 years ago by
gokberk
• 0
0
votes
2
replies
560
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 3.5 years ago by
Wei Shi
★ 3.5k • written 3.5 years ago by
hafiz.talhamalik
• 0
0
votes
1
reply
296
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
8 months ago
NIK
• 0
0
votes
1
reply
634
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 6 months ago by
Gordon Smyth
47k • written 6 months ago by
selmanurkeskin
• 0
0
votes
0
replies
82
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 10 weeks ago by
ATpoint
★ 2.1k • written 10 weeks ago by
Leon
• 0
0
votes
5
replies
1.3k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 4.0 years ago by
Gordon Smyth
47k • written 4.0 years ago by
leo_CD
• 0
28 results • Page
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Replies
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
by
Hervé Pagès
16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
by
Hervé Pagès
16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Sva and batch effect
by
Gordon Smyth
47k
(+1). I find that ComBat tends to introduce spurious differential expression so, you think there's a batch effect affecting the variances a…
Comment: Advice for the analysis of microarray data with limma
by
Gordon Smyth
47k
You mean references on orthogonal polynomials? Polynomial approximation is a classic topic in mathematics and statistics and there are many…
Comment: Limma-voom with inverse probability weights (similar to sample weights)
by
Gordon Smyth
47k
The potential problem isn't with empirical Bayes with the fact that the variance estimate from your method A linear model might not be mean…
Votes
Answer: Sva and batch effect
Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Limma-voom with inverse probability weights
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