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Showing :
Alignment
•
reset
0
votes
0
replies
80
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment
Biostrings
5 weeks ago
vonSkopnik
• 0
0
votes
1
reply
115
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment
Biostrings
7 weeks ago
潘晓光
• 0
0
votes
1
reply
289
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 12 weeks ago by
James W. MacDonald
62k • written 3 months ago by
Mohamed
• 0
0
votes
0
replies
233
views
Edit alignment in msa
alig
msa
Alignment
3 months ago
Luis
• 0
0
votes
2
replies
290
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
6 months ago • updated 5 months ago
sreekalasn
• 0
0
votes
0
replies
260
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
10 months ago
saira
• 0
0
votes
1
reply
356
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread
Alignment
updated 11 months ago by
Yang Liao
▴ 350 • written 11 months ago by
amytam2014
• 0
0
votes
0
replies
230
views
Pairwise alignment results with the original coordinates.
Biostrings
Alignment
12 months ago
Charles Plessy
▴ 170
0
votes
2
replies
459
views
BLAST-like alignment of a DNAString to a BSgenome?
Alignment
Genome
15 months ago
Charles Plessy
▴ 170
2
votes
2
replies
677
views
Rsubread doesn't output a .bai file
Rsubread
align
Alignment
updated 19 months ago by
Gordon Smyth
47k • written 19 months ago by
mike_flower
• 0
0
votes
5
replies
762
views
DECIPHER maximum allowable size
DECIPHER
Alignment
alig
updated 20 months ago by
Erik Wright
▴ 150 • written 21 months ago by
curiousmind007
• 0
0
votes
1
reply
530
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl
Alignment
QuasR
updated 24 months ago by
Michael Stadler
▴ 350 • written 24 months ago by
h.kozlowski
• 0
0
votes
3
replies
942
views
Rsubread unable to return alignments
Rsubread
Alignment
updated 2.2 years ago by
Yang Liao
▴ 350 • written 2.2 years ago by
Daniel
• 0
0
votes
2
replies
402
views
insufficient alignment
DECIPHER
Alignment
2.2 years ago
julius_vn
• 0
0
votes
2
replies
567
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation
Alignment
Gviz
2.2 years ago
Vaibhav
• 0
0
votes
3
replies
654
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS
LC-MS
LC-MS/MS
Alignment
updated 2.8 years ago by
Johannes Rainer
★ 2.0k • written 2.8 years ago by
ljveillon
• 0
0
votes
0
replies
443
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings
alignment
3.8 years ago
Juliet Hannah
▴ 360
1
vote
1
reply
1.2k
views
Tutorial:
How to download reference genomes using the RBioMart from ensembl?
BioMart
downloading reference genome
alignment
Tutorial
3.8 years ago
jcollidelcs
• 0
0
votes
9
replies
1.1k
views
visualizing alignment without realignment
msa
alignment
visualization
updated 3.9 years ago by
Martin Morgan
25k • written 3.9 years ago by
tim.ivanov.92
• 0
0
votes
0
replies
443
views
Multiple alignment solution for a character object of short fragments
r
alignment
3.9 years ago
r.tor
• 0
0
votes
9
replies
1.5k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
4.2 years ago
A
▴ 40
0
votes
0
replies
524
views
Quantifying reporter expression to validate sequencing
alignment
Fastq
fasta
4.2 years ago
A
▴ 40
2
votes
1
reply
689
views
Rsubread for microbiome data analysis: genome >4GB
alignment
rsubread
microbiome
updated 4.2 years ago by
Wei Shi
★ 3.5k • written 4.2 years ago by
W. Evan Johnson
▴ 840
0
votes
16
replies
3.0k
views
Error while using buildindex for human genome
rsubread
buildindex
fasta
alignment
4.3 years ago
writetoroopali
• 0
0
votes
0
replies
641
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM
samtools
pairwisealignment
alignment
blastn
4.5 years ago
ktehmsen
• 0
0
votes
0
replies
589
views
problem for finding relative Version GTF file for my .fa file
alignment
BWA
Burrows-Wheeler Alignment Tool
4.6 years ago
modarzi
▴ 10
1
vote
1
reply
1.7k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R
sequencing
alignment
rsamtools
mapping
updated 4.8 years ago by
James W. MacDonald
62k • written 4.8 years ago by
nginet
▴ 10
1
vote
2
replies
1.1k
views
RNA-seq read alignment best practices for low-input samples
limma
differential gene expression
rnaseq analysis
alignment
RSEM
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
goldberg.jm
▴ 10
0
votes
4
replies
727
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 5.1 years ago by
Hervé Pagès
16k • written 5.1 years ago by
dhwani2410
• 0
2
votes
4
replies
1.3k
views
running msa (msa) aborts R session
msa
alignment
r
software error
written 5.2 years ago by
ans74
• 0
0
votes
1
reply
848
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher
alignment
updated 5.3 years ago by
Erik Wright
▴ 10 • written 5.3 years ago by
emma.berdan
• 0
1
vote
4
replies
1.3k
views
How to find the end position of a read?
rsamtools
alignment
cigar
5.6 years ago
Frocha
▴ 10
0
votes
0
replies
718
views
Highlighting only GC mismatches in the Alignment track of Gviz
gviz
alignment
6.0 years ago
s8shcahk
• 0
2
votes
4
replies
827
views
plotting proteases digestion points in a protein
biostrings
iranges
sequence
alignment
protein
updated 6.0 years ago by
Michael Lawrence
11k • written 6.0 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
1
reply
908
views
How to remmove duplicated paired end alignments
alignment
duplicate
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
Frocha
▴ 10
0
votes
0
replies
820
views
Biostrings "global" alignment does NOT return a global alignment
biostrings
alignment
6.2 years ago
map2085
▴ 40
0
votes
0
replies
712
views
Figuring out what long decent Phred value unaligned reads are
rnaseq
alignment
6.3 years ago
Matthew Thornton
▴ 350
0
votes
16
replies
1.6k
views
Variance between runs of Rsubread
rsubread
alignment
reproducibility
6.3 years ago
Isaac Virshup
• 0
0
votes
3
replies
2.3k
views
Is there a package for peptide alignment with protein sequences?
Alignment
Alignment
updated 6.4 years ago by
contactbiostructure
• 0 • written 9.3 years ago by
Guest User
★ 12k
3
votes
4
replies
1.1k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread
rnaseq
alignment
updated 6.5 years ago by
Gordon Smyth
47k • written 6.5 years ago by
thomas.dobrenel
• 0
0
votes
4
replies
1.2k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR
rnaseq
alignment
splicemap
bowtie2
6.9 years ago
Gabriella
• 0
0
votes
3
replies
1.0k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap
QuasR
RNAseq
Alignment
updated 7.0 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 7.0 years ago by
tarek.mohamed
▴ 10
0
votes
1
reply
997
views
QuasR: spliced and unspliced alignment
quasr
alignment
updated 7.1 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 7.1 years ago by
nadia_boufaied
• 0
3
votes
1
reply
1.2k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error
rsubread
alignment
updated 7.1 years ago by
Wei Shi
★ 3.5k • written 7.2 years ago by
Thomas Carroll
▴ 420
0
votes
5
replies
1.3k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq
quasr
alignment
updated 7.1 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 7.2 years ago by
nadia_boufaied
• 0
0
votes
1
reply
1.1k
views
Counting SNPs where ambiguity codes represent heterozygosity.
Biostrings
SNPs
alignment
updated 7.5 years ago by
Hervé Pagès
16k • written 7.6 years ago by
ben.ward
▴ 30
0
votes
2
replies
3.2k
views
Bioconductor 2.12 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
Microarray
Coverage
Alignment
Annotation
GO
updated 7.6 years ago by
marksteve952
• 0 • written 9.8 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
6
replies
2.6k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster
quasR
genomicfeatures
genomicranges
alignment
updated 7.6 years ago by
Hervé Pagès
16k • written 7.6 years ago by
Fiona
▴ 70
0
votes
0
replies
1.4k
views
Clustering sequence on similarity using percentage identity matrix
alignment
clustering
7.6 years ago
Bade
▴ 310
2
votes
4
replies
5.7k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing
Alignment
DESeq
DESeq2
Sequencing
Alignment
DESeq
DESeq2
updated 7.7 years ago by
gaelgarcia
• 0 • written 8.7 years ago by
Guest User
★ 12k
50 results • Page
1 of 1
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Replies
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage
by
ayabalbaa1990
• 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object
by
shaimaa
• 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2
by
Basti
▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Comment: Atena package - error (new user)
by
beatriz.calvo
▴ 30
Hi Lalani, We have fixed the bug that lead to the error. The new version of the package (with the bug fixed) will be available in 24-48h. …
Answer: mas5calls function doesn't work; mirna40cdf problem
by
James W. MacDonald
62k
You cannot use `mas5calls` on a miRNA-4_0 array. There are no MM probes on that array, so it is not possible to get MAS-5.0 calls, because …
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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