Showing : featureCounts • reset
2
votes
2
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2.5k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 4.6 years ago by ▴ 450 • written 4.6 years ago by • 0
0
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0
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1.1k
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
5.0 years ago martinag.work • 0
1
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2
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4.7k
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
5.6 years ago chatterjee.arumoy ▴ 10
2
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3
replies
2.4k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
4
votes
2
replies
1.8k
views
bwa mem to feature Counts
bwa mem featureCounts
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by • 0
0
votes
2
replies
1.4k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 6.2 years ago by ★ 3.6k • written 6.2 years ago by • 0
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
2
replies
3.8k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
1
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1
reply
1.1k
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 6.4 years ago by 53k • written 6.4 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
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
1
vote
1
reply
4.1k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 6.5 years ago by ★ 3.6k • written 6.5 years ago by ▴ 10
7
votes
5
replies
5.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 60
2
votes
6
replies
2.7k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 6.6 years ago by ★ 3.6k • written 6.6 years ago by • 0
1
vote
2
replies
2.1k
views
Problem with importing text file in featureCounts
Rsubread featureCounts
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
3
votes
2
replies
2.9k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq featureCounts STAR minMQS mapping quality score
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 20
0
votes
5
replies
2.9k
views
featureCounts error : SAM_pairer_iterate_tags
subread featureCounts
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
3
votes
13
replies
4.0k
views
Rsubread- feature counts
annotation Rsubread featureCounts
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
1
vote
3
replies
1.8k
views
how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
6.8 years ago melkile26 • 0
0
votes
9
replies
4.0k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts Rsubread ggbio
updated 6.9 years ago by ★ 3.6k • written 6.9 years ago by ▴ 60
1
vote
1
reply
3.0k
views
Warning using feuture count related to GTF file
featurecounts
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
1
reply
1.3k
views
weired output with featurecount
featurecounts star
7.1 years ago roghaiyeh.safari • 0
0
votes
6
replies
2.2k
views
Options Request for FeatureCounts
featurecounts subread
updated 7.2 years ago by ★ 3.6k • written 7.2 years ago by • 0
0
votes
6
replies
4.1k
views
Error in designAndArgChecker(object, betaPrior) : variables in the design formula cannot have NA values
deseq2 featurecounts error message
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
4
votes
5
replies
2.0k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts rnaseq subread
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
3
votes
2
replies
3.7k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 7.3 years ago by 53k • written 7.3 years ago by • 0
4
votes
2
replies
6.0k
views
featureCounts for multiple features
featurecounts
updated 2.9 years ago by ▴ 20 • written 7.3 years ago by ▴ 10
1
vote
2
replies
2.2k
views
How to change sample names in featureCounts or edgeR
featurecounts edgeR
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 20
2
votes
3
replies
1.8k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 2.6 years ago by 53k • written 7.4 years ago by ▴ 20
0
votes
8
replies
4.6k
views
featureCounts Returns 0.0% successfully assigned fragments
rsubread featurecounts
7.4 years ago connor.geraghty • 0
0
votes
2
replies
4.1k
views
lncRNA annotation for featureCouns and STAR
lncRNA featureCounts STAR annotation
updated 7.4 years ago by ★ 3.6k • written 7.4 years ago by ▴ 10
4
votes
7
replies
3.5k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
6
votes
6
replies
7.9k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 3.0 years ago by ▴ 200 • written 7.4 years ago by ▴ 10
0
votes
4
replies
4.4k
views
featureCounts taking 4-10 hours per BAM file?
featurecounts r rnaseq
7.5 years ago octopuslegs11 • 0
1
vote
4
replies
2.0k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 7.7 years ago by ★ 3.6k • written 7.7 years ago by • 0
0
votes
1
reply
1.5k
views
featureCounts : limits on multioverlap (option -O)
featurecounts read counting
updated 7.7 years ago by 53k • written 7.7 years ago by • 0
0
votes
1
reply
1.7k
views
Rsubread Read Bam and filter reads by TAG field
Rsubread featurecounts featurerequest
7.8 years ago alessandro.pastore ▴ 20
0
votes
7
replies
3.0k
views
caught segfault when using featureCounts
rsubread featurecounts
7.9 years ago • updated 7.8 years ago Ge Tan ▴ 20
4
votes
15
replies
5.4k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 7.9 years ago by 43k • written 8.0 years ago by ▴ 10
5
votes
3
replies
6.8k
views
Rsubread counting peaks ATACseq
Rsubread atac-seq narrowpeaks featurecounts
updated 7.9 years ago by ★ 3.6k • written 7.9 years ago by ▴ 90
3
votes
1
reply
3.0k
views
Explainnation of featureCounts in-built annotation?
rnaseq annotation featurecounts
updated 8.0 years ago by ★ 3.6k • written 8.0 years ago by ▴ 20
3
votes
1
reply
1.6k
views
featureCounts in-built annotation doesn't match BioMart annotation?
rnaseq annotation featurecounts biomart
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 20
4
votes
8
replies
2.2k
views
When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
rnaseq featurecounts edger deseq2
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 20
0
votes
1
reply
920
views
Feature Count annotation file problem
annotation featurecounts
8.1 years ago fatemeh.kaveh • 0
0
votes
6
replies
2.6k
views
Rsubread featureCounts with byReadGroup
rsubread featurecounts
updated 8.1 years ago by ▴ 450 • written 8.1 years ago by ▴ 20
1
vote
1
reply
2.4k
views
featureCounts using 3'UTR as genome
featurecounts R
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
2
votes
14
replies
9.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 2.7 years ago by ▴ 20 • written 8.2 years ago by ▴ 120
1
vote
5
replies
4.0k
views
using paired end and single end data in featurecounts
featurecounts rsubread
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
0
votes
3
replies
3.2k
views
featureCount and bam
featurecounts
8.3 years ago Morris ▴ 10
0
votes
3
replies
3.4k
views
read count summed over exons is greater tham the gene-level read count using featureCounts
rsubread featurecounts exon mRNAseq
updated 8.4 years ago by ★ 3.6k • written 8.4 years ago by ▴ 10
136 results • Page 2 of 3
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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