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Showing :
alignment
•
reset
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 5 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
0
votes
2
replies
618
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 9 months ago by
Wei Shi
★ 3.6k • written 9 months ago by
amanda.gutierrez
• 0
0
votes
2
replies
713
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray
Alignment
Biostrings
written 12 months ago by
sandmann.t
▴ 70
0
votes
1
reply
417
views
Generate false reads for testing
mgu74bv2cdf
Software
Alignment
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Franck RICHARD
• 0
0
votes
3
replies
591
views
Multitasking and Rbwa
Rbwa
Alignment
written 11 months ago by
Franck RICHARD
• 0
0
votes
0
replies
390
views
Align to reference genome
Alignment
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Antonio
• 0
0
votes
0
replies
626
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
14 months ago
jsharif
• 0
0
votes
0
replies
625
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment
Biostrings
16 months ago
vonSkopnik
• 0
0
votes
1
reply
681
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment
Biostrings
17 months ago
潘晓光
• 0
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
0
votes
1
reply
1.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Mohamed
▴ 30
0
votes
0
replies
708
views
Edit alignment in msa
alig
msa
Alignment
19 months ago
Luis
• 0
0
votes
2
replies
841
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
21 months ago • updated 20 months ago
sreekalasn
• 0
0
votes
0
replies
725
views
SUBREAD Aligning reads with reference genome - Error in align The number of input file names is different from the number of output file names.
align
Alignment
subread
2.1 years ago
saira
• 0
0
votes
1
reply
843
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread
Alignment
updated 2.2 years ago by
Yang Liao
▴ 380 • written 2.2 years ago by
amytam2014
• 0
0
votes
0
replies
658
views
Pairwise alignment results with the original coordinates.
Biostrings
Alignment
2.3 years ago
Charles Plessy
▴ 180
0
votes
2
replies
1.0k
views
BLAST-like alignment of a DNAString to a BSgenome?
Alignment
Genome
2.6 years ago • updated 2.5 years ago
Charles Plessy
▴ 180
2
votes
2
replies
1.3k
views
Rsubread doesn't output a .bai file
Rsubread
align
Alignment
updated 2.9 years ago by
Gordon Smyth
50k • written 2.9 years ago by
mike_flower
• 0
0
votes
5
replies
1.5k
views
DECIPHER maximum allowable size
DECIPHER
Alignment
alig
updated 3.0 years ago by
Erik Wright
▴ 150 • written 3.0 years ago by
curiousmind007
▴ 10
0
votes
1
reply
1.0k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl
Alignment
QuasR
updated 3.3 years ago by
Michael Stadler
▴ 350 • written 3.3 years ago by
h.kozlowski
• 0
0
votes
3
replies
1.7k
views
Rsubread unable to return alignments
Rsubread
Alignment
updated 3.4 years ago by
Yang Liao
▴ 380 • written 3.4 years ago by
Daniel
• 0
0
votes
2
replies
794
views
insufficient alignment
DECIPHER
Alignment
3.5 years ago
julius_vn
• 0
0
votes
2
replies
1000
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation
Alignment
Gviz
3.5 years ago
Vaibhav
• 0
0
votes
3
replies
1.5k
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS
LC-MS
LC-MS/MS
Alignment
updated 4.0 years ago by
Johannes Rainer
★ 2.0k • written 4.0 years ago by
ljveillon
• 0
0
votes
0
replies
755
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings
alignment
5.0 years ago
Juliet Hannah
▴ 360
1
vote
1
reply
2.0k
views
Tutorial:
How to download reference genomes using the RBioMart from ensembl?
BioMart
downloading reference genome
alignment
Tutorial
5.1 years ago
jcollidelcs
• 0
0
votes
9
replies
1.9k
views
visualizing alignment without realignment
msa
alignment
visualization
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
tim.ivanov.92
• 0
0
votes
0
replies
699
views
Multiple alignment solution for a character object of short fragments
r
alignment
5.2 years ago
r.tor
• 0
0
votes
9
replies
2.6k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
5.4 years ago
A
▴ 40
0
votes
0
replies
880
views
Quantifying reporter expression to validate sequencing
alignment
Fastq
fasta
5.5 years ago
A
▴ 40
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment
rsubread
microbiome
updated 5.5 years ago by
Wei Shi
★ 3.6k • written 5.5 years ago by
W. Evan Johnson
▴ 850
0
votes
16
replies
4.4k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
5.5 years ago
writetoroopali
• 0
0
votes
0
replies
1.1k
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM
samtools
pairwisealignment
alignment
blastn
5.7 years ago
ktehmsen
• 0
0
votes
0
replies
1.1k
views
problem for finding relative Version GTF file for my .fa file
alignment
BWA
Burrows-Wheeler Alignment Tool
5.9 years ago
modarzi
▴ 10
1
vote
1
reply
2.7k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R
sequencing
alignment
rsamtools
mapping
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
nginet
▴ 10
1
vote
2
replies
1.7k
views
RNA-seq read alignment best practices for low-input samples
limma
differential gene expression
rnaseq analysis
alignment
RSEM
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
goldberg.jm
▴ 10
0
votes
4
replies
1.4k
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 6.4 years ago by
Hervé Pagès
16k • written 6.4 years ago by
dhwani2410
• 0
0
votes
1
reply
1.2k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher
alignment
updated 6.6 years ago by
Erik Wright
▴ 10 • written 6.6 years ago by
emma.berdan
• 0
1
vote
4
replies
2.2k
views
How to find the end position of a read?
rsamtools
alignment
cigar
6.9 years ago
Frocha
▴ 20
0
votes
0
replies
1.0k
views
Highlighting only GC mismatches in the Alignment track of Gviz
gviz
alignment
7.3 years ago
s8shcahk
• 0
2
votes
4
replies
1.3k
views
plotting proteases digestion points in a protein
biostrings
iranges
sequence
alignment
protein
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
1
reply
1.4k
views
How to remmove duplicated paired end alignments
alignment
duplicate
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
Frocha
▴ 20
0
votes
0
replies
1.2k
views
Biostrings "global" alignment does NOT return a global alignment
biostrings
alignment
7.5 years ago
map2085
▴ 40
0
votes
0
replies
1.1k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq
alignment
7.5 years ago
Matthew Thornton
▴ 350
0
votes
16
replies
2.5k
views
Variance between runs of Rsubread
rsubread
alignment
reproducibility
7.6 years ago
Isaac Virshup
• 0
0
votes
3
replies
3.1k
views
Is there a package for peptide alignment with protein sequences?
Alignment
Alignment
updated 7.7 years ago by
contactbiostructure
• 0 • written 10.6 years ago by
Guest User
★ 13k
3
votes
4
replies
1.5k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread
rnaseq
alignment
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
thomas.dobrenel
• 0
0
votes
4
replies
1.7k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR
rnaseq
alignment
splicemap
bowtie2
8.2 years ago
Gabriella
• 0
0
votes
3
replies
1.5k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap
QuasR
RNAseq
Alignment
updated 8.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.3 years ago by
tarek.mohamed
▴ 10
0
votes
1
reply
1.4k
views
QuasR: spliced and unspliced alignment
quasr
alignment
updated 8.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 8.3 years ago by
nadia_boufaied
• 0
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Comment: SingleR Label.Ont
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nice post nice post nice post nice post nice post
Comment: Extremely small p-values using Limma for proteomic data
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65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
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42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
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by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
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Comment: Extremely small p-values using Limma for proteomic data
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