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Showing :
SubRead
•
reset
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
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
1.8k
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
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
0
votes
1
reply
940
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 5.0 years ago by
gokberk
• 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
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
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
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
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
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
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
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
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
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
1
vote
5
replies
4.6k
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
0
votes
1
reply
764
views
Subread installation on Linux ARM64
subread
featureCounts
updated 14 months ago by
Yang Liao
▴ 380 • written 14 months ago by
Keyu
• 0
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
2
votes
2
replies
759
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
18 months ago
dario.beraldi
• 0
4
votes
3
replies
1.2k
views
RSubread in cygwin
subread
5.3 years ago
Diana
▴ 10
0
votes
0
replies
712
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
2.0 years ago
saira
• 0
0
votes
1
reply
823
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
23 months ago
NIK
• 0
4
votes
4
replies
4.9k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
1
vote
1
reply
720
views
Threads on Subread
Slurm
Subread
updated 2.0 years ago by
ATpoint
★ 4.0k • written 2.0 years ago by
sha-ked
• 0
1
vote
4
replies
1.6k
views
Subread installation
subread
featureCounts
2.0 years ago
Lucy
▴ 60
0
votes
0
replies
611
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
571
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
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
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
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
30 results • Page
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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