Showing : Alignment • reset
0
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2
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887
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R session aborts after running align function on Rsubread
Rsubread Alignment
updated 16 months ago by ★ 3.6k • written 16 months ago by • 0
0
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2
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990
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 20 months ago by ▴ 70
0
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1
reply
593
views
Generate false reads for testing
mgu74bv2cdf Software Alignment
updated 18 months ago by 67k • written 18 months ago by • 0
0
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3
replies
872
views
Multitasking and Rbwa
Rbwa Alignment
written 19 months ago by • 0
0
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0
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516
views
Align to reference genome
Alignment
updated 21 months ago by 67k • written 21 months ago by • 0
0
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0
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849
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
22 months ago agamemnon • 0
0
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0
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864
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
24 months ago vonSkopnik • 0
0
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2
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985
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 9 weeks ago by ▴ 20 • written 2.0 years ago by • 0
0
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1
reply
2.0k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.1 years ago by 67k • written 2.1 years ago by ▴ 30
0
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0
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914
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Edit alignment in msa
alig msa Alignment
2.2 years ago Luis • 0
0
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2
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1.0k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
2.4 years ago • updated 2.3 years ago sreekalasn • 0
0
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0
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903
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
2.7 years ago saira • 0
0
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1
reply
1.1k
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 2.8 years ago by ▴ 450 • written 2.8 years ago by • 0
0
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0
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822
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.9 years ago Charles Plessy ▴ 180
0
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2
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1.3k
views
BLAST-like alignment of a DNAString to a BSgenome?
Alignment Genome
3.2 years ago Charles Plessy ▴ 180
2
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2
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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
0
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5
replies
1.9k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 3.6 years ago by ▴ 150 • written 3.6 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl Alignment QuasR
updated 3.9 years ago by ▴ 350 • written 3.9 years ago by • 0
0
votes
3
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2.1k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 4.1 years ago by ▴ 450 • written 4.1 years ago by • 0
0
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2
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989
views
insufficient alignment
DECIPHER Alignment
4.1 years ago julius_vn • 0
0
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2
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1.2k
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation Alignment Gviz
4.1 years ago Vaibhav • 0
0
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3
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1.9k
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS LC-MS LC-MS/MS Alignment
updated 4.6 years ago by ★ 2.1k • written 4.6 years ago by • 0
0
votes
0
replies
902
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
5.6 years ago Juliet Hannah ▴ 360
1
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1
reply
2.5k
views
Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.7 years ago jcollidelcs • 0
0
votes
9
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2.3k
views
visualizing alignment without realignment
msa alignment visualization
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
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0
replies
794
views
Multiple alignment solution for a character object of short fragments
r alignment
5.8 years ago r.tor • 0
0
votes
9
replies
3.1k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
6.0 years ago A ▴ 40
0
votes
0
replies
1.0k
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
6.1 years ago A ▴ 40
2
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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
0
votes
16
replies
4.8k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
6.2 years ago writetoroopali • 0
0
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0
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1.3k
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM samtools pairwisealignment alignment blastn
6.4 years ago ktehmsen • 0
0
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0
replies
1.3k
views
problem for finding relative Version GTF file for my .fa file
alignment BWA Burrows-Wheeler Alignment Tool
6.5 years ago modarzi ▴ 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 6.7 years ago by 67k • written 6.7 years ago by ▴ 10
1
vote
2
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2.1k
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
0
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4
replies
1.6k
views
Query with Biostrings pairwise alignment output positon
biostrings alignment pairwisealignment
updated 7.0 years ago by 16k • written 7.0 years ago by • 0
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
0
votes
1
reply
1.4k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher alignment
updated 7.2 years ago by ▴ 10 • written 7.2 years ago by • 0
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
0
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0
replies
1.1k
views
Highlighting only GC mismatches in the Alignment track of Gviz
gviz alignment
7.9 years ago s8shcahk • 0
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
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
0
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0
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1.3k
views
Biostrings "global" alignment does NOT return a global alignment
biostrings alignment
8.1 years ago map2085 ▴ 40
0
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0
replies
1.2k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
8.2 years ago Matthew Thornton ▴ 380
0
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16
replies
2.9k
views
Variance between runs of Rsubread
rsubread alignment reproducibility
8.2 years ago Isaac Virshup • 0
0
votes
3
replies
3.4k
views
Is there a package for peptide alignment with protein sequences?
Alignment Alignment
updated 8.3 years ago by • 0 • written 11.2 years ago by ★ 13k
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
0
votes
4
replies
1.9k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR rnaseq alignment splicemap bowtie2
8.8 years ago Gabriella • 0
0
votes
3
replies
1.7k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap QuasR RNAseq Alignment
updated 8.9 years ago by ▴ 400 • written 8.9 years ago by ▴ 10
0
votes
1
reply
1.6k
views
QuasR: spliced and unspliced alignment
quasr alignment
updated 8.9 years ago by ▴ 400 • written 8.9 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
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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