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SubRead
•
reset
4
votes
4
replies
4.9k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
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
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
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
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
4
replies
3.0k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.6 years ago by
Patrick
• 0
1
vote
1
reply
2.9k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.0 years ago by
Wei Shi
★ 3.6k • written 5.0 years ago by
aurel.nagy
▴ 10
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
5
replies
2.4k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
abano
• 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
0
votes
5
replies
2.1k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
leo_CD
• 0
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.2 years ago
Lucy
▴ 60
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
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
1
vote
4
replies
1.6k
views
Subread installation
subread
featureCounts
2.0 years ago
Lucy
▴ 60
0
votes
6
replies
1.5k
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
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
4
votes
3
replies
1.2k
views
RSubread in cygwin
subread
5.3 years ago
Diana
▴ 10
4
votes
2
replies
1.2k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Jonathan Griffiths
▴ 90
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
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
0
votes
1
reply
941
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 5.0 years ago by
Yang Liao
▴ 380 • written 5.1 years ago by
gokberk
• 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
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
2
votes
2
replies
762
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
18 months ago
dario.beraldi
• 0
1
vote
1
reply
721
views
Threads on Subread
Slurm
Subread
updated 2.0 years ago by
ATpoint
★ 4.0k • written 2.0 years ago by
sha-ked
• 0
0
votes
0
replies
716
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
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
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
30 results • Page
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Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
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
by
ATpoint
★ 4.0k
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
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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