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subread
•
reset
0
votes
0
replies
384
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
9 months ago
yao hua
• 0
0
votes
1
reply
531
views
Subread installation on Linux ARM64
subread
featureCounts
updated 10 months ago by
Yang Liao
▴ 380 • written 10 months ago by
Keyu
• 0
1
vote
1
reply
1.3k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 12 months ago by
Gordon Smyth
49k • written 12 months ago by
Sara
• 0
0
votes
0
replies
398
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 12 months ago by
ATpoint
★ 3.6k • written 12 months ago by
Leon
• 0
2
votes
2
replies
567
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
13 months ago
dario.beraldi
• 0
0
votes
1
reply
2.4k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 17 months ago by
Gordon Smyth
49k • written 17 months ago by
selmanurkeskin
• 0
0
votes
1
reply
655
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
18 months ago
NIK
• 0
3
votes
11
replies
2.9k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
19 months ago
Sarah_piggy
▴ 10
1
vote
1
reply
613
views
Threads on Subread
Slurm
Subread
updated 20 months ago by
ATpoint
★ 3.6k • written 20 months ago by
sha-ked
• 0
1
vote
4
replies
1.2k
views
Subread installation
subread
featureCounts
20 months ago
Lucy
▴ 60
0
votes
0
replies
610
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
20 months ago
saira
• 0
1
vote
5
replies
1.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
22 months ago • updated 21 months ago
Lucy
▴ 60
4
votes
4
replies
4.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.1 years ago
k___
▴ 20
1
vote
1
reply
960
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.3 years ago by
Wei Shi
★ 3.5k • written 2.3 years ago by
dario.beraldi
• 0
1
vote
5
replies
3.9k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 4 months ago by
Yang Liao
▴ 380 • written 2.4 years ago by
s.muroy
▴ 10
2
votes
2
replies
1.6k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 2.8 years ago by
Yang Liao
▴ 380 • written 2.8 years ago by
Jason
• 0
1
vote
5
replies
2.0k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 3.4 years ago by
James W. MacDonald
64k • written 3.4 years ago by
abano
• 0
3
votes
4
replies
2.7k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.3 years ago by
Patrick
• 0
0
votes
2
replies
913
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 4.4 years ago by
Wei Shi
★ 3.5k • written 4.4 years ago by
hafiz.talhamalik
• 0
1
vote
2
replies
2.3k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 4.4 years ago by
Gordon Smyth
49k • written 4.4 years ago by
algenubi81
• 0
4
votes
2
replies
1.1k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 4.6 years ago by
Gordon Smyth
49k • written 4.6 years ago by
Jonathan Griffiths
▴ 90
1
vote
1
reply
2.6k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 4.7 years ago by
Wei Shi
★ 3.5k • written 4.7 years ago by
aurel.nagy
▴ 10
0
votes
1
reply
812
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 4.7 years ago by
Yang Liao
▴ 380 • written 4.7 years ago by
gokberk
• 0
0
votes
5
replies
1.9k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 4.8 years ago by
Gordon Smyth
49k • written 4.8 years ago by
leo_CD
• 0
4
votes
3
replies
1.1k
views
RSubread in cygwin
subread
4.9 years ago
Diana
▴ 10
0
votes
6
replies
1.3k
views
Options Request for FeatureCounts
featurecounts
subread
updated 5.3 years ago by
Wei Shi
★ 3.5k • written 5.3 years ago by
Leon
• 0
4
votes
5
replies
1.2k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 5.3 years ago by
Gordon Smyth
49k • written 5.3 years ago by
rogangrant
• 0
3
votes
2
replies
2.9k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 5.4 years ago by
Gordon Smyth
49k • written 5.4 years ago by
jennyl.smith12
• 0
3
votes
2
replies
2.2k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 6.6 years ago by
Wei Shi
★ 3.5k • written 6.6 years ago by
jma1991
▴ 70
2
votes
2
replies
1.3k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 7.9 years ago by
Wei Shi
★ 3.5k • written 7.9 years ago by
Vivek.b
▴ 100
30 results • Page
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Replies
Answer: WGCNA documentation not available
by
James W. MacDonald
64k
Although people sometimes ask questions about WGCNA on this support site, it's not a Bioconductor package and therefore off-topic. Peter La…
Comment: ATACseqQC shiftGAlignmentsList() problem
by
Ou, Jianhong
★ 1.3k
try: `gal1 <- shiftGAlignmentsList(gal, outbam='3-AL1_Tn5_shift.bam')`. I will try to figure out why the memory is so high.
Comment: ATACseqQC shiftGAlignmentsList() problem
by
jfmay
• 0
Thanks for your response. The version of ATACseqQC I'm using is 1.26.0. I tried to set bigFile=TRUE. The resulting object *gal1* still ends…
Answer: biomaRt_getBM_Failed to collect lazy table
by
James W. MacDonald
64k
That's an old bug that you should be able to fix by updating. I can't remember what package, although `db_collect` comes from `dbplyr` (and…
Comment: rDGIdb package inconsistency with web interface
by
christopherjamessteel1990
• 0
I went on https://www.dgidb.org/api and searched "RPS3A" and got the below result. Not sure how you got something different. There is certa…
Votes
Comment: DESeq2 - batch, condition and tissue information
Answer: ScRNAseq analysis scran :: quickcluster Error
Comment: Ensembl down???
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and
Comment: Ensembl down???
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