Showing : Alignment • reset
6
votes
3
replies
2.3k
views
Possible bug in Rsubread Phred-Score read
rsubread bug alignment
updated 10.1 years ago by ★ 3.6k • written 10.1 years ago by ▴ 20
5
votes
8
replies
6.5k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam sam alignment biostrings
9.8 years ago ben.ward ▴ 30
5
votes
12
replies
8.1k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 9.9 years ago by 52k • written 10.6 years ago by ★ 1.0k
3
votes
4
replies
1.8k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread rnaseq alignment
updated 8.4 years ago by 52k • written 8.4 years ago by • 0
3
votes
1
reply
1.7k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error rsubread alignment
updated 9.0 years ago by ★ 3.6k • written 9.0 years ago by ▴ 420
3
votes
3
replies
1.8k
views
Reading large DNA alignments and keeping polymorphic sites
sequence alignment biostrings
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 30
2
votes
1
reply
2.4k
views
Sequence Distance matrix with large sequences
Alignment Alignment
updated 11.1 years ago by 16k • written 11.1 years ago by ▴ 20
2
votes
1
reply
1.7k
views
How to remmove duplicated paired end alignments
alignment duplicate
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
2
votes
1
reply
1.3k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 6.1 years ago by ★ 3.6k • written 6.1 years ago by ▴ 870
2
votes
4
replies
1.6k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ★ 1.5k
2
votes
0
replies
1.1k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment Alignment
14.9 years ago Coghlan, Avril ▴ 190
2
votes
4
replies
7.4k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 9.5 years ago by • 0 • written 10.5 years ago by ★ 13k
2
votes
4
replies
2.4k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.0 years ago by • 0
2
votes
5
replies
1.4k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment GO Cancer BSgenome BSgenome Alignment GO Cancer BSgenome BSgenome
updated 11.5 years ago by 25k • written 11.5 years ago by ★ 13k
2
votes
2
replies
1.6k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 3.5 years ago by 52k • written 3.5 years ago by • 0
1
vote
1
reply
2.4k
views
Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.7 years ago jcollidelcs • 0
1
vote
2
replies
2.0k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
1
vote
1
reply
3.4k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 6.6 years ago by 67k • written 6.6 years ago by ▴ 10
1
vote
2
replies
2.4k
views
Finding mismatches between reads and reference sequence
bsgenome cigar alignment
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 40
1
vote
4
replies
2.6k
views
How to find the end position of a read?
rsamtools alignment cigar
7.5 years ago Frocha ▴ 20
1
vote
0
replies
1.5k
views
Genome editing analysis with Illumina sequencing
indel sequencing alignment
9.6 years ago Merienne Nicolas ▴ 120
1
vote
5
replies
5.0k
views
DiffBind error
Alignment DiffBind Alignment DiffBind
updated 11.9 years ago by ★ 5.2k • written 11.9 years ago by ▴ 280
1
vote
1
reply
3.1k
views
Creat PWM from Alignment with Gaps
Alignment Cancer Alignment Cancer
updated 11.2 years ago by ▴ 250 • written 11.2 years ago by 16k
1
vote
1
reply
1.4k
views
Rsubread for paired end SOLID sequencing
Sequencing Alignment convert Rsubread Sequencing Alignment convert Rsubread
updated 11.3 years ago by ★ 3.6k • written 11.3 years ago by ▴ 50
1
vote
1
reply
2.3k
views
multiple threads on QuasR
Alignment GLAD QuasR Alignment GLAD QuasR
11.7 years ago • updated 11.6 years ago Michael Stadler ▴ 350
1
vote
3
replies
2.0k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 11.3 years ago by ★ 7.2k • written 11.3 years ago by ▴ 220
0
votes
2
replies
1.2k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 15.2 years ago by 25k • written 15.2 years ago by ▴ 40
0
votes
1
reply
1.5k
views
removal of outliers in matrix
Alignment Alignment
updated 17.1 years ago by ▴ 450 • written 17.1 years ago by ▴ 20
0
votes
1
reply
1.9k
views
getSequence: difference between coding_gene_flank and 5utr
Alignment Alignment
updated 15.2 years ago by ▴ 660 • written 15.2 years ago by ▴ 220
0
votes
1
reply
882
views
possible bug in extendReads() in package chipseq
Alignment ShortRead Alignment ShortRead
updated 15.1 years ago by 25k • written 15.1 years ago by ▴ 40
0
votes
0
replies
1.1k
views
R: Pairwise Sequence Alignments
miRNA Alignment biomaRt miRNA Alignment biomaRt
15.4 years ago mauede@alice.it ▴ 870
0
votes
1
reply
3.8k
views
how deal with multiplicate affy probes?
Alignment mgu74av2 probe affy ASSIGN Alignment mgu74av2 probe affy ASSIGN
updated 20.6 years ago by ★ 5.5k • written 20.6 years ago by ▴ 50
0
votes
5
replies
1.9k
views
Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 11.8 years ago by ▴ 420 • written 11.8 years ago by ★ 11k
0
votes
1
reply
927
views
Pairwise Sequence Alignments
Alignment Alignment
updated 15.4 years ago by 21k • written 15.4 years ago by ▴ 870
0
votes
2
replies
1.2k
views
scoring matrices
Alignment Alignment
updated 15.4 years ago by ▴ 190 • written 15.4 years ago by ▴ 870
0
votes
2
replies
1.1k
views
AffyProbes and genome
Microarray Alignment Annotation Cancer probe affy Microarray Alignment Annotation Cancer
updated 19.6 years ago by ▴ 20 • written 19.6 years ago by ▴ 110
0
votes
0
replies
1.0k
views
visualization and alignment of affymetirx probe sequence to transcripts
Alignment probe Alignment probe
15.7 years ago shirley zhang ★ 1.0k
0
votes
1
reply
1.7k
views
Cell DNA content data normalization and gating
Alignment flowCore Alignment flowCore
updated 13.8 years ago by ▴ 240 • written 13.8 years ago by ▴ 10
0
votes
0
replies
797
views
visualization and alignment of affymetirx probe sequence to transcripts
Alignment probe Alignment probe
15.7 years ago shirley zhang ★ 1.0k
0
votes
1
reply
1.0k
views
limma imageplot
Alignment limma oligo Alignment limma oligo
updated 20.8 years ago by 52k • written 20.8 years ago by ▴ 90
0
votes
0
replies
1.3k
views
occurrence of rGADEM motifs (mattia pelizzola)
Alignment rGADEM MotIV Alignment rGADEM MotIV
13.4 years ago Mercier Eloi ▴ 60
0
votes
1
reply
1.1k
views
missing reads in alignerBAM
Alignment convert Alignment convert
updated 14.0 years ago by 25k • written 14.0 years ago by ▴ 90
0
votes
3
replies
1.7k
views
Genome position to miRNA or gene name
miRNA Alignment GO Cancer BSgenome BSgenome miRNA Alignment GO Cancer BSgenome BSgenome
updated 15.9 years ago by 25k • written 15.9 years ago by ★ 1.9k
0
votes
2
replies
2.6k
views
alignment & SNP calling
Alignment Alignment
updated 14.1 years ago by ▴ 810 • written 14.1 years ago by ▴ 90
0
votes
1
reply
1.2k
views
ShortRead qa() for BAM files?
Coverage Alignment ShortRead Coverage Alignment ShortRead
updated 14.2 years ago by 25k • written 14.2 years ago by ▴ 260
0
votes
0
replies
1.1k
views
How do I use biomaRt to get upstreamFlank Genomic Sequence for many Genomes?
Alignment biomaRt genomes Alignment biomaRt genomes
14.0 years ago Noah Dowell ▴ 410
0
votes
0
replies
1.3k
views
SAM warning
Biophysics Alignment Annotation Normalization Cancer hgu133plus2 probe affy vsn MBCB vsn
15.9 years ago elliot harrison ▴ 230
0
votes
3
replies
1.8k
views
Mapping microarray probes to the genome using findOverlaps
Alignment Annotation zebrafish probe Alignment Annotation zebrafish probe
updated 13.8 years ago by 21k • written 13.8 years ago by ▴ 140
0
votes
9
replies
2.1k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 13.8 years ago by 21k • written 13.8 years ago by 16k
0
votes
0
replies
825
views
post-doc position needed
Microarray Alignment Microarray Alignment
21.3 years ago Junwen wang ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Comment: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k
I agree that the current behavior is not entirely satisfactory and, indeed, it has prevented me from using the junction read counts from fe…
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Sorry, I didn't see the added response to your original answer. I think that would be a great idea; a novel junction to annot…
Comment: Cannot install GO.db and org.Hs.eg.db by Gabriel • 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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