Showing : Alignment • reset
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Memory error while running alignments
DECIPHER Alignment
updated 22 days ago by ▴ 150 • written 3 months ago by • 0
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2
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1.2k
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R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.2 years ago by ★ 3.6k • written 2.2 years ago by • 0
0
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2
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1.3k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.5 years ago by ▴ 70
0
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1
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776
views
Generate false reads for testing
mgu74bv2cdf Software Alignment
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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3
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1.1k
views
Multitasking and Rbwa
Rbwa Alignment
written 2.5 years ago by • 0
0
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0
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632
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Align to reference genome
Alignment
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
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0
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1.1k
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.7 years ago agamemnon • 0
0
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0
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1.1k
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Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.9 years ago vonSkopnik • 0
0
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2
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1.3k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 13 months ago by ▴ 20 • written 2.9 years ago by • 0
0
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1
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2.8k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 30
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0
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1.1k
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Edit alignment in msa
alig msa Alignment
3.1 years ago Luis • 0
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2
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1.4k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.3 years ago • updated 3.2 years ago sreekalasn • 0
0
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0
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1.1k
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
3.6 years ago saira • 0
0
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1
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1.3k
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 3.7 years ago by ▴ 450 • written 3.7 years ago by • 0
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0
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1.1k
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.8 years ago Charles Plessy ▴ 180
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2
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1.5k
views
BLAST-like alignment of a DNAString to a BSgenome?
Alignment Genome
4.1 years ago • updated 4.0 years ago Charles Plessy ▴ 180
2
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2
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2.0k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
0
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5
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2.3k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 4.5 years ago by ▴ 150 • written 4.5 years ago by ▴ 10
0
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1
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1.5k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl Alignment QuasR
updated 4.8 years ago by ▴ 350 • written 4.8 years ago by • 0
0
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3
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2.5k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 4.9 years ago by ▴ 450 • written 4.9 years ago by • 0
0
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2
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1.2k
views
insufficient alignment
DECIPHER Alignment
5.0 years ago julius_vn • 0
0
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2
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1.4k
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation Alignment Gviz
5.0 years ago Vaibhav • 0
0
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3
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2.6k
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS LC-MS LC-MS/MS Alignment
updated 5.5 years ago by ★ 2.1k • written 5.5 years ago by • 0
0
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0
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1.1k
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
6.5 years ago Juliet Hannah ▴ 360
0
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9
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2.8k
views
visualizing alignment without realignment
msa alignment visualization
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
0
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0
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916
views
Multiple alignment solution for a character object of short fragments
r alignment
6.7 years ago r.tor • 0
0
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9
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3.7k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
6.9 years ago A ▴ 60
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0
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1.2k
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
7.0 years ago A ▴ 60
2
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1
reply
1.5k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 7.0 years ago by ★ 3.6k • written 7.0 years ago by ▴ 870
0
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16
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5.5k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
7.0 years ago writetoroopali • 0
0
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0
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1.6k
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM samtools pairwisealignment alignment blastn
7.2 years ago ktehmsen • 0
0
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0
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1.6k
views
problem for finding relative Version GTF file for my .fa file
alignment BWA Burrows-Wheeler Alignment Tool
7.4 years ago modarzi ▴ 10
1
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1
reply
4.3k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 7.5 years ago by 68k • written 7.5 years ago by ▴ 10
1
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2
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2.7k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 10
0
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4
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2.0k
views
Query with Biostrings pairwise alignment output positon
biostrings alignment pairwisealignment
updated 7.9 years ago by 16k • written 7.9 years ago by • 0
2
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4
replies
2.8k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.9 years ago by • 0
0
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1
reply
1.6k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher alignment
updated 8.1 years ago by ▴ 10 • written 8.1 years ago by • 0
1
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4
replies
3.1k
views
How to find the end position of a read?
rsamtools alignment cigar
8.4 years ago Frocha ▴ 20
0
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0
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1.3k
views
Highlighting only GC mismatches in the Alignment track of Gviz
gviz alignment
8.8 years ago s8shcahk • 0
2
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4
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1.9k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ★ 1.5k
2
votes
1
reply
2.2k
views
How to remmove duplicated paired end alignments
alignment duplicate
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 20
0
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0
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1.5k
views
Biostrings "global" alignment does NOT return a global alignment
biostrings alignment
9.0 years ago map2085 ▴ 40
0
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0
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1.4k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
9.0 years ago Matthew Thornton ▴ 380
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16
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3.5k
views
Variance between runs of Rsubread
rsubread alignment reproducibility
9.1 years ago Isaac Virshup • 0
0
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3
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3.8k
views
Is there a package for peptide alignment with protein sequences?
Alignment Alignment
updated 9.2 years ago by • 0 • written 12.1 years ago by ★ 13k
3
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4
replies
2.1k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread rnaseq alignment
updated 9.3 years ago by 53k • written 9.3 years ago by • 0
0
votes
4
replies
2.2k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR rnaseq alignment splicemap bowtie2
9.7 years ago Gabriella • 0
0
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3
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1.9k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap QuasR RNAseq Alignment
updated 9.8 years ago by ▴ 400 • written 9.8 years ago by ▴ 10
0
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1
reply
1.8k
views
QuasR: spliced and unspliced alignment
quasr alignment
updated 9.8 years ago by ▴ 400 • written 9.8 years ago by • 0
3
votes
1
reply
1.8k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error rsubread alignment
updated 9.9 years ago by ★ 3.6k • written 9.9 years ago by ▴ 420
208 results • Page 1 of 5
Recent ...
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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