Showing : Rsubread • reset
1
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2
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1.6k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
3.5 years ago Chise ▴ 10
3
votes
11
replies
5.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.5 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 3.6 years ago by 53k • written 3.6 years ago by • 0
2
votes
1
reply
1.6k
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 20
0
votes
1
reply
1.3k
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 3.7 years ago by ▴ 450 • written 3.7 years ago by • 0
1
vote
5
replies
3.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.7 years ago Lucy ▴ 60
5
votes
6
replies
5.1k
views
Error in Rsubread featureCounts
Rsubread
3.7 years ago Zhaoxu • 0
2
votes
2
replies
8.4k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.8 years ago Chise ▴ 10
0
votes
2
replies
2.5k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 4.0 years ago by ▴ 450 • written 4.0 years ago by • 0
1
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8
replies
5.2k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
4.0 years ago v.merino.nicolas ▴ 10
0
votes
1
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1.2k
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 4.0 years ago by ★ 3.6k • written 4.0 years ago by • 0
2
votes
2
replies
2.0k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 4.3 years ago by 53k • written 4.3 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
4.4 years ago • updated 4.3 years ago Konstantinos Yeles ▴ 90
0
votes
2
replies
1.7k
views
Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
4.6 years ago jbono ▴ 10
2
votes
2
replies
2.5k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 4.7 years ago by ▴ 450 • written 4.7 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 4.6 years ago by ★ 3.6k • written 4.7 years ago by • 0
0
votes
10
replies
2.5k
views
Rsubread ComplexIndels
complexindelsindels Rsubread
4.7 years ago Hilary ▴ 40
0
votes
3
replies
2.5k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 4.9 years ago by ▴ 450 • written 4.9 years ago by • 0
5
votes
6
replies
6.4k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 4.9 years ago by • 0 • written 7.6 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 5.0 years ago by 68k • written 5.0 years ago by • 0
0
votes
0
replies
1.1k
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
5.0 years ago martinag.work • 0
5
votes
11
replies
2.4k
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error Rsubread
updated 5.4 years ago by 53k • written 5.4 years ago by • 0
2
votes
8
replies
4.4k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 3.5 years ago by ★ 3.4k • written 5.5 years ago by • 0
3
votes
5
replies
2.1k
views
featureCounts chrAliases not working as expected
Rsubread
updated 5.5 years ago by ▴ 450 • written 5.5 years ago by • 0
1
vote
2
replies
2.5k
views
Rsubread buildindex error
Rsubread
updated 5.6 years ago by ★ 3.6k • written 5.6 years ago by ▴ 10
1
vote
8
replies
3.2k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
5.6 years ago • updated 10 months ago bryan.penning • 0
0
votes
4
replies
1.9k
views
segfault "memory not mapped" using align from Rsubread
Rsubread align
5.6 years ago Joseph Fass ▴ 70
4
votes
4
replies
2.4k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
5.6 years ago Konstantinos Yeles ▴ 90
1
vote
12
replies
2.2k
views
negative one "-1" values in index files using Rsubread
software error rsubread
updated 5.6 years ago by ▴ 450 • written 5.6 years ago by • 0
0
votes
1
reply
899
views
Rsubread: using shared memory for index while aligning with forked processes
rsubread
updated 5.8 years ago by ★ 3.6k • written 5.8 years ago by • 0
2
votes
6
replies
3.7k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 5.9 years ago by ▴ 450 • written 5.9 years ago by • 0
5
votes
6
replies
2.3k
views
Rsubread malloc(): memory corruption
Rsubread malloc align
updated 6.0 years ago by 53k • written 6.2 years ago by ▴ 90
1
vote
1
reply
1.2k
views
Replicating bowtie2 alignment parameters with Rsubread
Rsubread
updated 6.1 years ago by ★ 3.6k • written 6.1 years ago by • 0
2
votes
3
replies
1.4k
views
Rsubread CIGAR output M only?
Rsubread cigar
updated 6.1 years ago by 53k • written 6.1 years ago by • 0
2
votes
7
replies
3.2k
views
Rsubread requests longread mode for shotgun RNAseq data
Rsubread counting RNA-seq
updated 4.4 years ago by ▴ 450 • written 6.1 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 4.1 years ago by ▴ 450 • written 6.1 years ago by • 0
2
votes
6
replies
3.1k
views
Install Rsubread in win10, failed, how to proceed?
rsubread windows10 rtools
updated 6.1 years ago by ▴ 450 • written 8.3 years ago by ▴ 200
11
votes
1
reply
1.5k
views
News: Rsubread now available for Windows
rsubread News
6.2 years ago • updated 6.1 years ago Gordon Smyth 53k
1
vote
2
replies
2.1k
views
Rsubread package not available?
Rsubread BiocInstaller
updated 6.2 years ago by 53k • written 13.9 years ago by ▴ 410
4
votes
3
replies
5.4k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 6.3 years ago by ★ 3.6k • written 6.3 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 6.4 years ago by ★ 3.6k • written 6.4 years ago by • 0
0
votes
1
reply
1.3k
views
Is possible to use NOISeq with counts from RSubread?
noiseq rsubread tophat bowtie bowtie2
6.4 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 6.4 years ago by ★ 3.6k • written 6.4 years ago by ▴ 60
2
votes
1
reply
2.5k
views
Rsubread installation problem
Rsubread BiocParallel
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 20
1
vote
1
reply
1.1k
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 40
5
votes
11
replies
5.4k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 3.5 years ago by ▴ 10 • written 6.5 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 6.5 years ago by ★ 3.6k • written 6.5 years ago by ▴ 60
3
votes
7
replies
2.6k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
4
votes
2
replies
1.7k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread Rsubread
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 90
7
votes
5
replies
5.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 60
208 results • Page 2 of 5
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Replies
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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