Showing : Rsubread • reset
2
votes
2
replies
148
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
4
votes
5
replies
433
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
3 months ago • updated 9 weeks ago Konstantinos Yeles ▴ 70
0
votes
2
replies
233
views
Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
5 months ago jbono ▴ 10
2
votes
2
replies
270
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 6 months ago by ▴ 260 • written 6 months ago by • 0
0
votes
6
replies
367
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
updated 5 months ago by ★ 3.3k • written 6 months ago by • 0
0
votes
10
replies
463
views
Rsubread ComplexIndels
complexindelsindels Rsubread
7 months ago Hilary ▴ 20
5
votes
26
replies
2.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 9 months ago by ▴ 260 • written 6.5 years ago by 7.6k
0
votes
3
replies
326
views
Rsubread unable to return alignments
Rsubread Alignment
updated 9 months ago by ▴ 260 • written 9 months ago by • 0
5
votes
6
replies
1.7k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 10 months ago by • 0 • written 3.4 years ago by • 0
0
votes
3
replies
1.4k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 10 months ago by 58k • written 10 months ago by • 0
0
votes
0
replies
178
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
10 months ago martinag.work • 0
5
votes
11
replies
463
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error Rsubread
updated 15 months ago by 43k • written 15 months ago by • 0
2
votes
5
replies
286
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 16 months ago by ★ 3.3k • written 16 months ago by • 0
3
votes
5
replies
322
views
featureCounts chrAliases not working as expected
Rsubread
updated 16 months ago by ▴ 260 • written 17 months ago by • 0
1
vote
2
replies
220
views
Rsubread buildindex error
Rsubread
updated 17 months ago by ★ 3.3k • written 17 months ago by • 0
0
votes
4
replies
355
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 18 months ago by ▴ 260 • written 18 months ago by • 0
0
votes
4
replies
300
views
segfault "memory not mapped" using align from Rsubread
Rsubread align
18 months ago Joseph Fass ▴ 70
4
votes
4
replies
251
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
18 months ago Konstantinos Yeles ▴ 70
0
votes
12
replies
359
views
negative one "-1" values in index files using Rsubread
software error rsubread
updated 18 months ago by ▴ 260 • written 18 months ago by • 0
0
votes
1
reply
202
views
Rsubread: using shared memory for index while aligning with forked processes
rsubread
updated 20 months ago by ★ 3.3k • written 20 months ago by • 0
2
votes
6
replies
515
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 21 months ago by ▴ 260 • written 21 months ago by • 0
5
votes
6
replies
537
views
Rsubread malloc(): memory corruption
Rsubread malloc align
updated 23 months ago by 43k • written 2.1 years ago by ▴ 70
1
vote
1
reply
307
views
Replicating bowtie2 alignment parameters with Rsubread
Rsubread
updated 23 months ago by ★ 3.3k • written 23 months ago by • 0
2
votes
3
replies
273
views
Rsubread CIGAR output M only?
Rsubread cigar
updated 24 months ago by 43k • written 24 months ago by • 0
2
votes
7
replies
762
views
Rsubread requests longread mode for shotgun RNAseq data
Rsubread counting RNA-seq
updated 3 months ago by ▴ 260 • written 24 months ago by • 0
2
votes
5
replies
659
views
"ERROR: cannot create temp file" when using buildindex from Rsubread
software error Rsubread buildindex
updated 6 days ago by ▴ 260 • written 24 months ago by • 0
2
votes
6
replies
1.6k
views
Install Rsubread in win10, failed, how to proceed?
rsubread windows10 rtools
updated 2.0 years ago by ▴ 260 • written 4.2 years ago by ▴ 200
11
votes
1
reply
412
views
News: Rsubread now available for Windows
rsubread News
2.1 years ago • updated 2.0 years ago Gordon Smyth 43k
1
vote
2
replies
897
views
Rsubread package not available?
Rsubread BiocInstaller
updated 2.1 years ago by 43k • written 9.8 years ago by ▴ 410
4
votes
3
replies
1.4k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 2.2 years ago by ★ 3.3k • written 2.2 years ago by ▴ 80
1
vote
3
replies
637
views
Killed 9 on macOS Mojave for Rsubread buildindex
Rsubread buildindex killed 9 Mojave
updated 2.2 years ago by ★ 3.3k • written 2.3 years ago by • 0
0
votes
1
reply
272
views
Is possible to use NOISeq with counts from RSubread?
noiseq rsubread tophat bowtie bowtie2
2.3 years ago Marcelo Laia ▴ 440
2
votes
3
replies
454
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 2.3 years ago by ★ 3.3k • written 2.3 years ago by ▴ 50
2
votes
1
reply
636
views
Rsubread installation problem
Rsubread BiocParallel
updated 2.3 years ago by 43k • written 2.4 years ago by ▴ 10
1
vote
1
reply
263
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 30
3
votes
9
replies
1.3k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 2.4 years ago by ★ 3.3k • written 2.4 years ago by ▴ 100
5
votes
6
replies
542
views
Improving the performance of the align function from Rsubread for old Roche454 reads
align rsubread roche454 rnaseq
updated 2.4 years ago by ★ 3.3k • written 2.4 years ago by ▴ 50
3
votes
7
replies
735
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
4
votes
2
replies
464
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread Rsubread
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 30
7
votes
5
replies
1.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 50
12
votes
7
replies
548
views
No method for coercing this S4 class to a vector, as trying to import my own data rather than using SRA in the workflow RnaSeqGeneEdgeRQL
rnaseqgeneedgerql shortread Rsubread
updated 2.5 years ago by ▴ 60 • written 2.5 years ago by ▴ 50
2
votes
6
replies
676
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 2.5 years ago by ★ 3.3k • written 2.5 years ago by • 0
1
vote
2
replies
386
views
Problem with importing text file in featureCounts
Rsubread featureCounts
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
3
votes
4
replies
470
views
Featurecount -- normalized Path error
path Rsubread
updated 2.6 years ago by • 0 • written 2.7 years ago by • 0
3
votes
13
replies
1.1k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
votes
2
replies
777
views
Data import with read.delim
limma rsubread
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
9
replies
890
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
2.8 years ago A ▴ 40
0
votes
9
replies
1.1k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 2.8 years ago by ★ 3.3k • written 2.8 years ago by ▴ 40
2
votes
1
reply
430
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 2.9 years ago by ★ 3.3k • written 2.9 years ago by ▴ 840
0
votes
16
replies
1.8k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
2.9 years ago writetoroopali • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Volcano plots of DEGs from Swish are weird by Qin ▴ 10
Thans for your reply. I'm sorry for reply so late, because I didn't getting any messages in my email. I will read details of the vignette.
Comment: At least one covariate is confounded with batch! Please remove confounded covari by NewBioInfo • 0
Thank you, James. I was indeed using the wrong matrix. The `nonExtimable` did give me the column name which was causing the issue but I do …
Comment: Returning to edgeR version 3.26.1? by Gordon Smyth 43k
I don't think that any changes to edgeR between 3.26.1 and 3.26.8 could have caused the changes that you show.
Comment: Returning to edgeR version 3.26.1? by mvanhorn • 0
Thank you very much for your reply! Our project is a reanalysis of large sets of RNA-seq data to identify circular RNAs using the CIRIquan…
Comment: "full model matrix is less than full rank" by ATpoint ▴ 840
My best guess is that young and old are not "young" or "old" but include some hidden whitespaces like " young" or "old ". That would then m…
Votes
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: Swish direction of comparison based on order of factors
Comment: Gradient dotplot
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
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