Showing : featureCounts • reset
0
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2
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2.9k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.2 years ago by ▴ 80
0
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0
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210
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
5 weeks ago • updated 4 weeks ago Gordon Smyth 48k
0
votes
2
replies
243
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understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 weeks ago by 63k • written 8 weeks ago by • 0
1
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1
reply
282
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 10 weeks ago by ▴ 380 • written 10 weeks ago by • 0
0
votes
1
reply
361
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 4 months ago by ★ 3.5k • written 5 months ago by • 0
0
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0
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214
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
5 months ago barrypraveen • 0
2
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9
replies
883
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featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
7 months ago • updated 6 months ago Hilary ▴ 30
0
votes
2
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510
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 7 months ago by ★ 3.5k • written 10 months ago by • 0
0
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0
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263
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
7 months ago yao hua • 0
0
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1
reply
416
views
Subread installation on Linux ARM64
subread featureCounts
updated 8 months ago by ▴ 380 • written 8 months ago by • 0
0
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1
reply
290
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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 8 months ago by ★ 1.3k • written 8 months ago by • 0
3
votes
3
replies
1.3k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 8 months ago by 48k • written 8 months ago by • 0
0
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1
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1.0k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 10 months ago by ★ 1.3k • written 10 months ago by • 0
1
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1
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1.1k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 10 months ago by 48k • written 10 months ago by • 0
0
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0
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310
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Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 10 months ago by ★ 3.4k • written 10 months ago by • 0
2
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3
replies
686
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 10 months ago by 48k • written 10 months ago by • 0
2
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2
replies
463
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
11 months ago dario.beraldi • 0
0
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0
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314
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
11 months ago rridley3 • 0
0
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2
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923
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
13 months ago KMS ▴ 10
0
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1
reply
2.0k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 14 months ago by 48k • written 14 months ago by • 0
0
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1
reply
515
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fetaure counts err
featurecounts
updated 14 months ago by ★ 3.5k • written 15 months ago by • 0
0
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1
reply
550
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
16 months ago NIK • 0
1
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1
reply
1.0k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 16 months ago by 48k • written 16 months ago by • 0
2
votes
1
reply
1.1k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 10
0
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4
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1.3k
views
featureCounts: 0% successfully assigned fragments
featureCounts
16 months ago KMS ▴ 10
1
vote
4
replies
973
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
17 months ago Chise ▴ 10
3
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11
replies
2.6k
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The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
17 months ago Sarah_piggy ▴ 10
1
vote
4
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1.1k
views
Subread installation
subread featureCounts
17 months ago Lucy ▴ 60
1
vote
5
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1.4k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
20 months ago • updated 19 months ago Lucy ▴ 60
2
votes
2
replies
4.3k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
21 months ago Chise ▴ 10
4
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4
replies
3.6k
views
FeatureCounts
counts subread RNASeq featurecounts
23 months ago k___ ▴ 20
0
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2
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1.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 12 months ago by • 0 • written 2.1 years ago by • 0
1
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1
reply
853
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 2.2 years ago by ★ 3.5k • written 2.2 years ago by • 0
1
vote
5
replies
3.5k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 10 weeks ago by ▴ 380 • written 2.3 years ago by ▴ 10
4
votes
5
replies
1.6k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.3 years ago • updated 2.2 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.5k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 2.6 years ago by ▴ 380 • written 2.6 years ago by • 0
6
votes
26
replies
4.9k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.8 years ago by ▴ 380 • written 8.6 years ago by 7.8k
0
votes
0
replies
554
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
2.9 years ago martinag.work • 0
1
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2
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2.9k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
3.5 years ago chatterjee.arumoy ▴ 10
2
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3
replies
1.6k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 3.9 years ago by 63k • written 3.9 years ago by • 0
4
votes
2
replies
943
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.0 years ago by ★ 1.3k • written 4.0 years ago by • 0
0
votes
2
replies
827
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.2 years ago by ★ 3.5k • written 4.2 years ago by • 0
4
votes
3
replies
3.8k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.2 years ago by ★ 3.5k • written 4.3 years ago by ▴ 80
1
vote
2
replies
2.1k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 4.2 years ago by 48k • written 4.2 years ago by • 0
1
vote
1
reply
710
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by ▴ 40
5
votes
11
replies
3.2k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 17 months ago by ▴ 10 • written 4.5 years ago by ▴ 120
3
votes
7
replies
1.6k
views
Rsubread inbuilt annotation
rsubread featureCounts
updated 4.4 years ago by 48k • written 4.4 years ago by • 0
1
vote
1
reply
2.4k
views
featureCounts for ATAC-seq
subread featurecounts atac
updated 4.5 years ago by ★ 3.5k • written 4.5 years ago by ▴ 10
7
votes
5
replies
3.2k
views
featureCounts returning a matrix of counts full of 0...
featureCounts rnaseq Rsubread
updated 4.5 years ago by 48k • written 4.5 years ago by ▴ 60
2
votes
6
replies
1.5k
views
featurecounts Rsubread ERROR on exon_id
R error software error Rsubread featurecounts
updated 4.5 years ago by ★ 3.5k • written 4.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results by James W. MacDonald 63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences by Hervé Pagès 16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results by camillab. ▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
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