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SubRead
•
reset
0
votes
0
replies
629
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
797
views
Subread installation on Linux ARM64
subread
featureCounts
updated 15 months ago by
Yang Liao
▴ 380 • written 15 months ago by
Keyu
• 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
584
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 17 months ago by
ATpoint
★ 4.1k • written 17 months ago by
Leon
• 0
2
votes
2
replies
779
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
18 months ago
dario.beraldi
• 0
0
votes
1
reply
3.3k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
selmanurkeskin
• 0
0
votes
1
reply
848
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
23 months ago
NIK
• 0
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.1 years ago • updated 2.0 years ago
Sarah_piggy
▴ 10
1
vote
1
reply
730
views
Threads on Subread
Slurm
Subread
updated 2.1 years ago by
ATpoint
★ 4.1k • written 2.1 years ago by
sha-ked
• 0
1
vote
4
replies
1.6k
views
Subread installation
subread
featureCounts
2.1 years ago
Lucy
▴ 60
0
votes
0
replies
725
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
2.1 years ago
saira
• 0
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.2 years ago
Lucy
▴ 60
4
votes
4
replies
5.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
1
vote
1
reply
1.2k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.8 years ago by
Wei Shi
★ 3.6k • written 2.8 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 2.9 years ago by
s.muroy
▴ 10
2
votes
2
replies
1.9k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.2 years ago by
Yang Liao
▴ 380 • written 3.2 years ago by
Jason
• 0
1
vote
5
replies
2.4k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
abano
• 0
3
votes
4
replies
3.1k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.7 years ago by
Patrick
• 0
0
votes
2
replies
1.1k
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 4.8 years ago by
Wei Shi
★ 3.6k • written 4.8 years ago by
hafiz.talhamalik
• 0
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
4
votes
2
replies
1.2k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
Jonathan Griffiths
▴ 90
1
vote
1
reply
3.0k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.1 years ago by
Wei Shi
★ 3.6k • written 5.1 years ago by
aurel.nagy
▴ 10
0
votes
1
reply
948
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 5.1 years ago by
Yang Liao
▴ 380 • written 5.1 years ago by
gokberk
• 0
0
votes
5
replies
2.2k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
leo_CD
• 0
4
votes
3
replies
1.3k
views
RSubread in cygwin
subread
5.3 years ago
Diana
▴ 10
0
votes
6
replies
1.6k
views
Options Request for FeatureCounts
featurecounts
subread
updated 5.7 years ago by
Wei Shi
★ 3.6k • written 5.7 years ago by
Leon
• 0
4
votes
5
replies
1.4k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
rogangrant
• 0
3
votes
2
replies
3.1k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
jennyl.smith12
• 0
3
votes
2
replies
2.4k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 7.0 years ago by
Wei Shi
★ 3.6k • written 7.0 years ago by
jma1991
▴ 70
2
votes
2
replies
1.4k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 8.3 years ago by
Wei Shi
★ 3.6k • written 8.3 years ago by
Vivek.b
▴ 100
30 results • Page
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Recent ...
Replies
Comment: deseq2 results
by
swbarnes2
★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code?
by
NATASHA
• 0
did you find a solution? I´m having the same problem
Comment: error
by
NATASHA
• 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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