Showing : featurecounts • reset
4
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8
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933
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Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
11 days ago • updated 3 days ago chris2.a.white • 0
0
votes
1
reply
477
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 9 days ago by 52k • written 9 months ago by • 0
1
vote
3
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524
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
10 weeks ago • updated 9 weeks ago yasmin.hilliam ▴ 10
0
votes
1
reply
226
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
11 weeks ago isaac.vock • 0
6
votes
3
replies
1.4k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 4 months ago by 67k • written 4 months ago by • 0
0
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4
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723
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
5 months ago • updated 4 months ago Jessica • 0
1
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2
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521
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
4 months ago Anke • 0
4
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2
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784
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
6 months ago Rachael • 0
2
votes
4
replies
956
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
8 months ago • updated 6 months ago isaac.vock • 0
1
vote
1
reply
654
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 9 months ago by ★ 3.6k • written 10 months ago by • 0
7
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28
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7.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 10 months ago by 52k • written 9.8 years ago by ★ 7.9k
0
votes
4
replies
877
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 10 months ago by 52k • written 10 months ago by • 0
4
votes
6
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1.1k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
11 months ago • updated 10 months ago isaac.vock • 0
0
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2
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4.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.4 years ago by ▴ 80
0
votes
0
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1.5k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
16 months ago • updated 15 months ago Gordon Smyth 52k
0
votes
2
replies
1.7k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 16 months ago by 67k • written 16 months ago by • 0
1
vote
1
reply
936
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 17 months ago by ▴ 450 • written 17 months ago by • 0
0
votes
1
reply
1.2k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 19 months ago by ★ 3.6k • written 20 months ago by • 0
0
votes
0
replies
619
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
20 months ago barrypraveen • 0
2
votes
9
replies
2.3k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
21 months ago Hilary ▴ 40
0
votes
2
replies
1.2k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 21 months ago by ★ 3.6k • written 2.1 years ago by • 0
0
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0
replies
867
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
22 months ago yao hua • 0
0
votes
1
reply
1.1k
views
Subread installation on Linux ARM64
subread featureCounts
updated 22 months ago by ▴ 450 • written 22 months ago by • 0
0
votes
1
reply
844
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2 featurecounts
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
3
votes
3
replies
4.5k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 23 months ago by 52k • written 23 months ago by • 0
0
votes
1
reply
2.9k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by • 0
1
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1
reply
2.8k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
0
votes
0
replies
763
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 2.1 years ago by ★ 4.6k • written 2.1 years ago by • 0
2
votes
3
replies
1.7k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
2
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2
replies
1.0k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
2.2 years ago dario.beraldi • 0
0
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0
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687
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.2 years ago rridley3 • 0
0
votes
2
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1.9k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
2.3 years ago KMS ▴ 20
0
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1
reply
4.3k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
0
votes
1
reply
987
views
fetaure counts err
featurecounts
updated 2.4 years ago by ★ 3.6k • written 2.5 years ago by • 0
0
votes
1
reply
1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.6 years ago NIK • 0
1
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1
reply
1.7k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
2
votes
1
reply
1.8k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by ▴ 10
0
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4
replies
2.1k
views
featureCounts: 0% successfully assigned fragments
featureCounts
2.6 years ago KMS ▴ 20
1
vote
4
replies
1.9k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.6 years ago Chise ▴ 10
3
votes
11
replies
4.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.7 years ago • updated 2.6 years ago Sarah_piggy ▴ 10
1
vote
4
replies
2.2k
views
Subread installation
subread featureCounts
2.7 years ago Lucy ▴ 60
1
vote
5
replies
2.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.9 years ago • updated 2.8 years ago Lucy ▴ 60
2
votes
2
replies
7.4k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.0 years ago Chise ▴ 10
4
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4
replies
5.8k
views
FeatureCounts
counts subread RNASeq featurecounts
3.1 years ago k___ ▴ 30
0
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2
replies
1.8k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 2.2 years ago by • 0 • written 3.3 years ago by • 0
1
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1
reply
1.5k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 3.4 years ago by ★ 3.6k • written 3.4 years ago by • 0
1
vote
5
replies
6.1k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 17 months ago by ▴ 450 • written 3.5 years ago by ▴ 10
4
votes
5
replies
2.6k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
3.5 years ago • updated 3.4 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
2.2k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.8 years ago by ▴ 450 • written 3.8 years ago by • 0
0
votes
0
replies
926
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
4.2 years ago martinag.work • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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