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subread
•
reset
0
votes
1
reply
66
views
Subread installation on Linux ARM64
subread
featureCounts
updated 1 day ago by
Yang Liao
▴ 350 • written 5 days ago by
Keyu
• 0
1
vote
1
reply
191
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 10 weeks ago by
Gordon Smyth
47k • written 11 weeks ago by
Sara
• 0
0
votes
0
replies
85
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 11 weeks ago by
ATpoint
★ 2.1k • written 11 weeks ago by
Leon
• 0
2
votes
2
replies
184
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
3 months ago
dario.beraldi
• 0
0
votes
1
reply
659
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
1
reply
302
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
8 months ago
NIK
• 0
3
votes
11
replies
1.2k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
9 months ago
Sarah_piggy
▴ 10
1
vote
1
reply
313
views
Threads on Subread
Slurm
Subread
updated 9 months ago by
ATpoint
★ 2.1k • written 9 months ago by
sha-ked
• 0
1
vote
4
replies
571
views
Subread installation
subread
featureCounts
10 months ago
Lucy
▴ 60
0
votes
0
replies
268
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
10 months ago
saira
• 0
1
vote
5
replies
785
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
12 months ago • updated 11 months ago
Lucy
▴ 60
4
votes
4
replies
2.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
15 months ago
k___
▴ 20
1
vote
1
reply
526
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
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
2
votes
2
replies
994
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 23 months ago by
Yang Liao
▴ 350 • written 23 months ago by
Jason
• 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
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
0
votes
2
replies
563
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
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
4
votes
2
replies
743
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
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
0
votes
1
reply
500
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 3.8 years ago by
Yang Liao
▴ 350 • written 3.8 years ago by
gokberk
• 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
4
votes
3
replies
817
views
RSubread in cygwin
subread
4.1 years ago
Diana
▴ 10
0
votes
6
replies
935
views
Options Request for FeatureCounts
featurecounts
subread
updated 4.4 years ago by
Wei Shi
★ 3.5k • written 4.5 years ago by
Leon
• 0
4
votes
5
replies
861
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 4.5 years ago by
Gordon Smyth
47k • written 4.5 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
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
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
29 results • Page
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Comment: TCGA: clinical data and expression data
by
sharifnstu1203002m
• 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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