Showing : featureCounts • reset
2
votes
7
replies
447
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
updated 1 day ago by ★ 3.6k • written 3 days ago by • 0
0
votes
1
reply
417
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 1 day ago by 52k • written 9 months ago by • 0
1
vote
3
replies
494
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
9 weeks ago • updated 8 weeks ago yasmin.hilliam ▴ 10
0
votes
1
reply
215
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
10 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 3 months ago by 67k • written 3 months ago by • 0
0
votes
4
replies
714
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
4 months ago Jessica • 0
1
vote
2
replies
508
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
4 months ago Anke • 0
2
votes
4
replies
942
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
8 months ago • updated 6 months ago isaac.vock • 0
4
votes
2
replies
761
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
6 months ago Rachael • 0
2
votes
2
replies
1.8k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 8 months ago by • 0 • written 8.5 years ago by ▴ 90
1
vote
1
reply
644
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
votes
28
replies
7.0k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 10 months ago by 52k • written 9.8 years ago by ★ 7.9k
4
votes
6
replies
1.1k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
10 months ago isaac.vock • 0
0
votes
4
replies
865
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 10 months ago by 52k • written 10 months ago by • 0
0
votes
2
replies
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
replies
1.5k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
15 months ago Gordon Smyth 52k
0
votes
2
replies
1.6k
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
5
replies
6.0k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 16 months ago by ▴ 450 • written 3.5 years ago by ▴ 10
1
vote
1
reply
930
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 17 months ago by ▴ 450 • written 17 months ago by • 0
0
votes
5
replies
2.6k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 17 months ago by ▴ 450 • written 7.6 years ago by • 0
3
votes
16
replies
20k
views
featureCounts - paired-end data
featurecounts rsubread
updated 18 months ago by • 0 • written 9.6 years ago by ▴ 140
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 19 months ago by • 0
0
votes
0
replies
614
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
3
replies
1.6k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 21 months ago by 52k • written 6.5 years ago by ▴ 20
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
1.1k
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 2.0 years ago by • 0
2
votes
14
replies
8.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 21 months ago by ▴ 20 • written 7.3 years ago by ▴ 120
0
votes
0
replies
864
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
839
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 22 months ago by ★ 1.4k • written 22 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
vote
1
reply
2.8k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.0 years ago by 52k • written 2.1 years ago by • 0
0
votes
0
replies
761
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
4
votes
2
replies
5.3k
views
featureCounts for multiple features
featurecounts
updated 2.1 years ago by ▴ 20 • written 6.4 years ago by ▴ 10
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
votes
2
replies
1.0k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
2.2 years ago dario.beraldi • 0
0
votes
0
replies
684
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.2 years ago rridley3 • 0
6
votes
6
replies
6.9k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 2.2 years ago by ▴ 200 • written 6.6 years ago by ▴ 10
0
votes
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
0
votes
2
replies
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
votes
1
reply
985
views
fetaure counts err
featurecounts
updated 2.4 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
votes
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
1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.6 years ago • updated 2.5 years ago NIK • 0
1
vote
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
0
votes
4
replies
2.1k
views
featureCounts: 0% successfully assigned fragments
featureCounts
2.6 years ago KMS ▴ 20
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
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
1.9k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.6 years ago Chise ▴ 10
5
votes
11
replies
4.5k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 2.7 years ago by ▴ 10 • written 5.7 years ago by ▴ 120
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Comment: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Answer: Need new version : tx2gene.gencode.v47.csv by Guido Hooiveld ★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Comment: Help using rtracklayer for gene ID extraction by Aichatou • 0
Hello, Please disregard the previous post. it's working now, i think. I am able to create the txdb object but I can't see all the other inf…
Comment: p value is 0, padj is 0 by Wirayatida • 0
Than you so much. My counts are 47,37 and 72 for mock. The treatment is 8153, 6723 and 8024.
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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