Showing : rsubread • reset
1
vote
2
replies
1.5k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
3.3 years ago Chise ▴ 10
3
votes
11
replies
5.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.4 years ago • updated 3.3 years ago Sarah_piggy ▴ 10
0
votes
1
reply
1.2k
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 3.4 years ago by 52k • written 3.4 years ago by • 0
2
votes
1
reply
1.5k
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 3.4 years ago by 52k • written 3.4 years ago by ▴ 20
0
votes
1
reply
1.2k
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 3.5 years ago by ▴ 450 • written 3.5 years ago by • 0
1
vote
5
replies
3.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.6 years ago • updated 3.5 years ago Lucy ▴ 60
5
votes
6
replies
5.0k
views
Error in Rsubread featureCounts
Rsubread
3.6 years ago Zhaoxu • 0
2
votes
2
replies
8.3k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.7 years ago Chise ▴ 10
0
votes
2
replies
2.4k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 3.8 years ago by ▴ 450 • written 3.8 years ago by • 0
1
vote
8
replies
5.0k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
3.8 years ago v.merino.nicolas ▴ 10
0
votes
1
reply
1.2k
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 3.9 years ago by ★ 3.6k • written 3.9 years ago by • 0
2
votes
2
replies
1.9k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 4.2 years ago by 52k • written 4.2 years ago by • 0
4
votes
5
replies
3.0k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
4.2 years ago • updated 4.1 years ago Konstantinos Yeles ▴ 90
0
votes
2
replies
1.6k
views
Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
4.4 years ago jbono ▴ 10
2
votes
2
replies
2.4k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 4.5 years ago by ▴ 450 • written 4.5 years ago by • 0
0
votes
6
replies
2.4k
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
updated 4.4 years ago by ★ 3.6k • written 4.5 years ago by • 0
0
votes
10
replies
2.4k
views
Rsubread ComplexIndels
complexindelsindels Rsubread
4.6 years ago • updated 4.5 years ago Hilary ▴ 40
0
votes
3
replies
2.4k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 4.8 years ago by ▴ 450 • written 4.8 years ago by • 0
5
votes
6
replies
6.3k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 4.8 years ago by • 0 • written 7.4 years ago by • 0
0
votes
3
replies
9.4k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
0
votes
0
replies
1.0k
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
4.9 years ago martinag.work • 0
5
votes
11
replies
2.3k
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error Rsubread
updated 5.2 years ago by 52k • written 5.2 years ago by • 0
2
votes
8
replies
4.3k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 3.4 years ago by ★ 3.4k • written 5.3 years ago by • 0
3
votes
5
replies
2.1k
views
featureCounts chrAliases not working as expected
Rsubread
updated 5.3 years ago by ▴ 450 • written 5.4 years ago by • 0
1
vote
2
replies
2.4k
views
Rsubread buildindex error
Rsubread
updated 5.4 years ago by ★ 3.6k • written 5.4 years ago by ▴ 10
1
vote
8
replies
3.1k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
5.5 years ago • updated 8 months ago bryan.penning • 0
0
votes
4
replies
1.8k
views
segfault "memory not mapped" using align from Rsubread
Rsubread align
5.4 years ago Joseph Fass ▴ 70
4
votes
4
replies
2.4k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
5.5 years ago Konstantinos Yeles ▴ 90
1
vote
12
replies
2.1k
views
negative one "-1" values in index files using Rsubread
software error rsubread
updated 5.5 years ago by ▴ 450 • written 5.5 years ago by • 0
0
votes
1
reply
867
views
Rsubread: using shared memory for index while aligning with forked processes
rsubread
updated 5.7 years ago by ★ 3.6k • written 5.7 years ago by • 0
2
votes
6
replies
3.6k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 5.8 years ago by ▴ 450 • written 5.8 years ago by • 0
5
votes
6
replies
2.3k
views
Rsubread malloc(): memory corruption
Rsubread malloc align
updated 5.9 years ago by 52k • written 6.0 years ago by ▴ 90
1
vote
1
reply
1.2k
views
Replicating bowtie2 alignment parameters with Rsubread
Rsubread
updated 5.9 years ago by ★ 3.6k • written 5.9 years ago by • 0
2
votes
3
replies
1.3k
views
Rsubread CIGAR output M only?
Rsubread cigar
updated 5.9 years ago by 52k • written 5.9 years ago by • 0
2
votes
7
replies
3.1k
views
Rsubread requests longread mode for shotgun RNAseq data
Rsubread counting RNA-seq
updated 4.2 years ago by ▴ 450 • written 5.9 years ago by • 0
2
votes
5
replies
2.9k
views
"ERROR: cannot create temp file" when using buildindex from Rsubread
software error Rsubread buildindex
updated 4.0 years ago by ▴ 450 • written 5.9 years ago by • 0
2
votes
6
replies
3.0k
views
Install Rsubread in win10, failed, how to proceed?
rsubread windows10 rtools
updated 6.0 years ago by ▴ 450 • written 8.2 years ago by ▴ 200
11
votes
1
reply
1.5k
views
News: Rsubread now available for Windows
rsubread News
6.0 years ago Gordon Smyth 52k
1
vote
2
replies
2.0k
views
Rsubread package not available?
Rsubread BiocInstaller
updated 6.0 years ago by 52k • written 13.8 years ago by ▴ 410
4
votes
3
replies
5.4k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 6.1 years ago by ★ 3.6k • written 6.2 years ago by ▴ 80
1
vote
3
replies
1.8k
views
Killed 9 on macOS Mojave for Rsubread buildindex
Rsubread buildindex killed 9 Mojave
updated 6.2 years ago by ★ 3.6k • written 6.2 years ago by • 0
0
votes
1
reply
1.2k
views
Is possible to use NOISeq with counts from RSubread?
noiseq rsubread tophat bowtie bowtie2
6.2 years ago Marcelo Laia ▴ 450
2
votes
3
replies
2.1k
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 6.2 years ago by ★ 3.6k • written 6.3 years ago by ▴ 60
2
votes
1
reply
2.4k
views
Rsubread installation problem
Rsubread BiocParallel
updated 6.3 years ago by 52k • written 6.3 years ago by ▴ 20
1
vote
1
reply
1.1k
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 6.3 years ago by 52k • written 6.3 years ago by ▴ 40
5
votes
11
replies
5.3k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 3.4 years ago by ▴ 10 • written 6.4 years ago by ▴ 120
5
votes
6
replies
2.1k
views
Improving the performance of the align function from Rsubread for old Roche454 reads
align rsubread roche454 rnaseq
updated 6.4 years ago by ★ 3.6k • written 6.4 years ago by ▴ 60
3
votes
7
replies
2.6k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 6.4 years ago by 52k • written 6.4 years ago by • 0
4
votes
2
replies
1.6k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread Rsubread
updated 6.4 years ago by 52k • written 6.4 years ago by ▴ 90
7
votes
5
replies
5.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 6.4 years ago by 52k • written 6.4 years ago by ▴ 60
208 results • Page 2 of 5
Recent ...
Replies
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to boczniak767 ▴ 740
Popular Question to Young Tae • 0
Popular Question to Robert Castelo ★ 3.4k
Popular Question to littlefishes20 ▴ 10
Locations • All
WEHI, Melbourne, Australia, 36 minutes ago
United States, 2 hours ago
Poland, 3 hours ago
United States, 3 hours ago
The city by the bay, 3 hours ago
Traffic: 623 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6