Showing : rsubread • reset
0
votes
0
replies
200
views
Blank gene_id in featureCounts
featureCounts Rsubread
3 months ago Meg • 0
5
votes
10
replies
2.3k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 8 months ago by • 0
0
votes
1
reply
844
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 6 months ago by 52k • written 6 months ago by ▴ 80
0
votes
1
reply
765
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 8 months ago by 52k • written 18 months ago by • 0
5
votes
4
replies
1.2k
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 8 months ago by ★ 4.9k • written 8 months ago by ▴ 10
2
votes
3
replies
1.1k
views
featureCounts segmentation fault with large chromosomes
Rsubread
10 months ago vkkodali ▴ 10
0
votes
0
replies
381
views
Rsubread - sublong function
pacbio sublong Rsubread
10 months ago thomas.heigl.ibk • 0
0
votes
1
reply
554
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
11 months ago isaac.vock • 0
0
votes
5
replies
1.1k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 10 months ago by ▴ 450 • written 11 months ago by • 0
1
vote
2
replies
826
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
13 months ago Anke • 0
0
votes
1
reply
530
views
featureCounts from Rsubread
Rsubread
updated 13 months ago by 52k • written 13 months ago by • 0
2
votes
4
replies
1.4k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
17 months ago • updated 14 months ago isaac.vock • 0
0
votes
6
replies
2.0k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
15 months ago atan • 0
0
votes
0
replies
438
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
16 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
914
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 17 months ago by ★ 3.6k • written 17 months ago by • 0
0
votes
1
reply
612
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 17 months ago by 52k • written 17 months ago by ▴ 180
1
vote
1
reply
1.0k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 18 months ago by ★ 3.6k • written 19 months ago by • 0
0
votes
0
replies
569
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
18 months ago thomas.heigl.ibk • 0
7
votes
28
replies
8.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 19 months ago by 52k • written 10.5 years ago by ★ 7.9k
1
vote
1
reply
855
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 18 months ago by ▴ 450 • written 19 months ago by ▴ 10
0
votes
4
replies
1.3k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 19 months ago by 52k • written 19 months ago by • 0
4
votes
6
replies
1.5k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
19 months ago isaac.vock • 0
1
vote
2
replies
1.1k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
19 months ago mirjanakessler • 0
0
votes
1
reply
732
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 21 months ago by 52k • written 21 months ago by • 0
2
votes
2
replies
1.7k
views
Long-read mode in featureCounts
Rsubread LongRead
22 months ago mmisak • 0
0
votes
2
replies
2.2k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
23 months ago Gregory • 0
0
votes
0
replies
772
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
23 months ago kthapa • 0
0
votes
2
replies
1.2k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
24 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
652
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 24 months ago by 52k • written 24 months ago by • 0
2
votes
3
replies
1.4k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.1 years ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.1k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.1 years ago by ★ 3.6k • written 2.1 years ago by • 0
0
votes
2
replies
2.3k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
1
reply
1.0k
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
1
reply
1.2k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.1 years ago by ▴ 450 • written 2.1 years ago by • 0
0
votes
2
replies
1.3k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by • 0
0
votes
1
reply
1.5k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.3 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
votes
0
replies
758
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.4 years ago barrypraveen • 0
1
vote
3
replies
1.4k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
2.4 years ago rmoorehe • 0
2
votes
9
replies
3.1k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.5 years ago Hilary ▴ 40
0
votes
2
replies
1.4k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.5 years ago by ★ 3.6k • written 2.8 years ago by • 0
2
votes
4
replies
3.1k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
0
votes
0
replies
700
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.6 years ago Wei • 0
3
votes
3
replies
6.6k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
2
votes
3
replies
2.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
0
votes
2
replies
1.2k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.1 years ago • updated 3.0 years ago sreekalasn • 0
13
votes
20
replies
5.0k
views
cellCounts() function floating point error
Rsubread
3.3 years ago • updated 3.1 years ago J-E • 0
0
votes
1
reply
1.6k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 3.3 years ago by ★ 4.9k • written 3.3 years ago by ▴ 10
1
vote
1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
1
vote
5
replies
1.8k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.4 years ago by 52k • written 3.3 years ago by • 0
1
vote
4
replies
2.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.3 years ago Chise ▴ 10
208 results • Page 1 of 5
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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