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Alignment
•
reset
0
votes
21
replies
6.5k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 4 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
0
votes
16
replies
1.9k
views
readGAlignmentPairs error
Alignment
Alignment
updated 10.6 years ago by
Hervé Pagès
16k • written 10.6 years ago by
Leonard Goldstein
▴ 80
0
votes
16
replies
2.5k
views
Variance between runs of Rsubread
rsubread
alignment
reproducibility
7.5 years ago
Isaac Virshup
• 0
0
votes
16
replies
4.3k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
5.5 years ago
writetoroopali
• 0
5
votes
12
replies
7.7k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq
Alignment
edgeR
sva
updated 9.2 years ago by
Gordon Smyth
50k • written 10.0 years ago by
shirley zhang
★ 1.0k
0
votes
11
replies
5.6k
views
Biostring: print sequence alignment to file
Alignment
Biostrings
Alignment
Biostrings
updated 12.0 years ago by
Thomas Girke
★ 1.7k • written 12.0 years ago by
Martin Preusse
▴ 100
0
votes
9
replies
1.9k
views
visualizing alignment without realignment
msa
alignment
visualization
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
tim.ivanov.92
• 0
0
votes
9
replies
2.5k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
5.4 years ago
A
▴ 40
0
votes
9
replies
1.8k
views
Mapping microarray probes to the genome using findOverlaps
Microarray
Alignment
Annotation
zebrafish
probe
Biostrings
GenomicFeatures
Microarray
updated 13.1 years ago by
Sean Davis
21k • written 13.1 years ago by
Hervé Pagès
16k
0
votes
8
replies
1.5k
views
memory exhausted for readAligned
Alignment
Alignment
updated 15.2 years ago by
Martin Morgan
25k • written 15.2 years ago by
Lana Schaffer
★ 1.3k
5
votes
8
replies
6.0k
views
Getting Aligned DNAStringSet from reference and BAM/SAM file(s)
bam
sam
alignment
biostrings
9.2 years ago
ben.ward
▴ 30
0
votes
8
replies
3.1k
views
Annotation files for bacterial genome RNAseq
Alignment
Annotation
ASSIGN
Alignment
Annotation
ASSIGN
updated 9.8 years ago by
James W. MacDonald
65k • written 9.8 years ago by
José Luis Lavín
▴ 80
0
votes
8
replies
2.0k
views
Rsubread alingner
Alignment
Yeast
Rsubread
Alignment
Yeast
Rsubread
13.0 years ago
Wei Shi
★ 3.6k
0
votes
7
replies
1.6k
views
MEDIPS error extending reads
Alignment
BSgenome
BSgenome
MEDIPS
Alignment
BSgenome
BSgenome
MEDIPS
updated 11.0 years ago by
Lukas Chavez
▴ 570 • written 11.0 years ago by
Stephen Turner
▴ 290
0
votes
7
replies
1.9k
views
about reduce function in GenomicRanges
Alignment
Alignment
12.3 years ago
Tarca, Adi
▴ 570
0
votes
7
replies
2.0k
views
QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
Alignment
Rattus norvegicus
BSgenome
BSgenome
QuasR
Alignment
Rattus norvegicus
BSgenome
updated 10.1 years ago by
Hervé Pagès
16k • written 10.1 years ago by
Guido Hooiveld
★ 3.9k
0
votes
7
replies
2.4k
views
obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1.0 array
Alignment
probe
Alignment
probe
updated 11.8 years ago by
James W. MacDonald
65k • written 11.8 years ago by
shirley zhang
★ 1.0k
0
votes
6
replies
3.2k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster
quasR
genomicfeatures
genomicranges
alignment
updated 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
Fiona
▴ 70
0
votes
6
replies
1.8k
views
Reading paired-end data into GRangesList
Alignment
Alignment
updated 12.5 years ago by
Paul Leo
▴ 970 • written 12.5 years ago by
Hubert Rehrauer
▴ 100
0
votes
6
replies
1.9k
views
Biostring: print sequence alignment to file
Alignment
Cancer
Biostrings
Alignment
Cancer
Biostrings
updated 11.8 years ago by
Martin Preusse
▴ 100 • written 11.8 years ago by
Hervé Pagès
16k
0
votes
6
replies
1.7k
views
separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment
BSgenome
safe
BSgenome
MEDIPS
Alignment
BSgenome
safe
BSgenome
MEDIPS
updated 10.3 years ago by
Lukas Chavez
▴ 570 • written 10.3 years ago by
Vining, Kelly
▴ 220
0
votes
5
replies
2.0k
views
filterBam
Alignment
Alignment
updated 10.8 years ago by
raffaele calogero
▴ 500 • written 10.8 years ago by
rcaloger
▴ 500
0
votes
5
replies
1.6k
views
Visualization of alignments with mismatch bases
SNP
Coverage
Alignment
Visualization
ggbio
SNP
Coverage
Alignment
Visualization
ggbio
updated 11.1 years ago by
Tengfei Yin
▴ 420 • written 11.1 years ago by
Michael Lawrence
★ 11k
1
vote
5
replies
4.7k
views
DiffBind error
Alignment
DiffBind
Alignment
DiffBind
updated 11.2 years ago by
Rory Stark
★ 5.1k • written 11.2 years ago by
José Luis Lavín
▴ 280
0
votes
5
replies
1.4k
views
DECIPHER maximum allowable size
DECIPHER
Alignment
alig
updated 2.9 years ago by
Erik Wright
▴ 150 • written 2.9 years ago by
curiousmind007
▴ 10
0
votes
5
replies
1.8k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq
quasr
alignment
updated 8.4 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.4 years ago by
nadia_boufaied
• 0
0
votes
5
replies
1.5k
views
easyRNASeq - error reading single chromosome bam
RNASeq
Alignment
BSgenome
BSgenome
RNASeq
Alignment
BSgenome
BSgenome
updated 12.2 years ago by
delhomme@embl.de
★ 1.2k • written 12.2 years ago by
Lescai, Francesco
▴ 380
2
votes
5
replies
1.3k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment
GO
Cancer
BSgenome
BSgenome
Alignment
GO
Cancer
BSgenome
BSgenome
updated 10.9 years ago by
Martin Morgan
25k • written 10.9 years ago by
Guest User
★ 13k
0
votes
5
replies
1.7k
views
A question about the function readGAlignmentPairs in GenomicRnages package
Alignment
Cancer
convert
GenomicAlignments
Alignment
Cancer
convert
GenomicAlignments
updated 10.0 years ago by
Hervé Pagès
16k • written 10.1 years ago by
Niu, Liang NIH/NIEHS [E]
▴ 50
0
votes
5
replies
1.4k
views
multiple locations for probeset in hgu133plus2CHRLOC vs. UCSC PSL data
Alignment
Annotation
hgu133plus2
Alignment
Annotation
hgu133plus2
updated 15.4 years ago by
Hervé Pagès
16k • written 15.4 years ago by
Bazeley, Peter
▴ 10
0
votes
5
replies
2.1k
views
MEDIPS.createSet error
Alignment
BSgenome
BSgenome
MEDIPS
Alignment
BSgenome
BSgenome
MEDIPS
updated 10.1 years ago by
Lukas Chavez
▴ 570 • written 10.1 years ago by
Vining, Kelly
▴ 220
0
votes
5
replies
1.1k
views
GappedAlignmentPairs requests
Alignment
Cancer
GenomicRanges
Alignment
Cancer
GenomicRanges
updated 11.8 years ago by
Michael Lawrence
★ 11k • written 11.8 years ago by
Hervé Pagès
16k
0
votes
5
replies
1.9k
views
unexpected behaviour of pairwiseAlignment() in Biostrings
Alignment
Biostrings
Alignment
Biostrings
13.8 years ago
Coghlan, Avril
▴ 190
0
votes
4
replies
1.5k
views
Howto annotate blast subject.id with AnnotationDbi
Alignment
GO
annotate
AnnotationDbi
Alignment
GO
annotate
AnnotationDbi
updated 10.9 years ago by
Marc Carlson
★ 7.2k • written 10.9 years ago by
Arnaud Mounier
▴ 40
0
votes
4
replies
1.7k
views
segfault for pairwiseAlignment
sequencing
software error
alignment
updated 9.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.6 years ago by
Taub, Margaret
▴ 10
0
votes
4
replies
1.7k
views
easyRNASeq error
Sequencing
Alignment
Annotation
Organism
BSgenome
biomaRt
BSgenome
easyRNASeq
Sequencing
12.1 years ago
delhomme@embl.de
★ 1.2k
2
votes
4
replies
2.1k
views
running msa (msa) aborts R session
msa
alignment
r
software error
written 6.4 years ago by
ans74
• 0
2
votes
4
replies
6.8k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing
Alignment
DESeq
DESeq2
Sequencing
Alignment
DESeq
DESeq2
updated 8.9 years ago by
gaelgarcia
• 0 • written 9.9 years ago by
Guest User
★ 13k
2
votes
4
replies
1.3k
views
plotting proteases digestion points in a protein
biostrings
iranges
sequence
alignment
protein
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
1.3k
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 6.3 years ago by
Hervé Pagès
16k • written 6.4 years ago by
dhwani2410
• 0
0
votes
4
replies
1.7k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR
rnaseq
alignment
splicemap
bowtie2
8.1 years ago
Gabriella
• 0
3
votes
4
replies
1.5k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread
rnaseq
alignment
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
thomas.dobrenel
• 0
0
votes
4
replies
1.7k
views
WIG coverage for Paired-end strand-specific RNA-Seq (PE ssRNA-Seq)
Alignment
Alignment
updated 10.5 years ago by
Michael Lawrence
★ 11k • written 10.5 years ago by
bach le
▴ 40
0
votes
4
replies
1.8k
views
nearly exact overlaps between GAlignmentPairs and GenomicRanges
Alignment
Alignment
9.7 years ago
Georg Otto
▴ 120
1
vote
4
replies
2.2k
views
How to find the end position of a read?
rsamtools
alignment
cigar
6.8 years ago
Frocha
▴ 20
0
votes
3
replies
2.8k
views
MEDIPS, GRanges, IRanges error processing BAM file
Alignment
BSgenome
PROcess
BSgenome
IRanges
MEDIPS
Alignment
BSgenome
PROcess
BSgenome
updated 10.7 years ago by
Lukas Chavez
▴ 570 • written 10.7 years ago by
Jonathan Ellis
▴ 40
3
votes
3
replies
1.6k
views
Reading large DNA alignments and keeping polymorphic sites
sequence
alignment
biostrings
updated 9.3 years ago by
Hervé Pagès
16k • written 9.4 years ago by
ben.ward
▴ 30
1
vote
3
replies
1.7k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment
Annotation
Organism
Schizosaccharomyces pombe
biomaRt
AnnotationForge
Alignment
updated 10.7 years ago by
Marc Carlson
★ 7.2k • written 10.7 years ago by
Marco Blanchette
▴ 220
0
votes
3
replies
1.4k
views
edgeR: mixing technical replicates from Illumina HiSeq and MiSeq
Sequencing
Alignment
GO
edgeR
DESeq2
updated 9.6 years ago by
Ryan C. Thompson
★ 7.9k • written 9.6 years ago by
Nick N
▴ 60
0
votes
3
replies
1.4k
views
homopolymer gap extension penalty in Biostrings
Sequencing
Alignment
GO
Cancer
Sequencing
Alignment
GO
Cancer
updated 12.1 years ago by
Noah Hoffman
▴ 10 • written 12.1 years ago by
Hervé Pagès
16k
50 results • Page
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Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
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Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
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