Showing : Alignment • reset
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Memory error while running alignments
DECIPHER Alignment
5 weeks ago Mihir • 0
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2
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1.1k
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R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.1 years ago by ★ 3.6k • written 2.1 years ago by • 0
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2
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1.3k
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.4 years ago by ▴ 70
0
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1
reply
750
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Generate false reads for testing
mgu74bv2cdf Software Alignment
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
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3
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1.1k
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Multitasking and Rbwa
Rbwa Alignment
written 2.3 years ago by • 0
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0
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616
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Align to reference genome
Alignment
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
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0
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1.0k
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.6 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
2.7 years ago vonSkopnik • 0
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2
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1.2k
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Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 11 months ago by ▴ 20 • written 2.8 years ago by • 0
0
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1
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2.7k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.9 years ago by 68k • written 2.9 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
2.9 years ago Luis • 0
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2
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1.2k
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Rsubread align --R session aborts
RNA Alignment Rsubread
3.1 years ago sreekalasn • 0
0
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0
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1.1k
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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
3.4 years ago saira • 0
0
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1
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1.2k
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 3.5 years ago by ▴ 450 • written 3.5 years ago by • 0
0
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0
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1.0k
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.6 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
3.9 years ago Charles Plessy ▴ 180
2
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2
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1.9k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
0
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5
replies
2.2k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 4.3 years ago by ▴ 150 • written 4.3 years ago by ▴ 10
0
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1
reply
1.5k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl Alignment QuasR
updated 4.6 years ago by ▴ 350 • written 4.6 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 4.8 years ago by ▴ 450 • written 4.8 years ago by • 0
0
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2
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1.2k
views
insufficient alignment
DECIPHER Alignment
4.9 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
4.9 years ago Vaibhav • 0
0
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3
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2.5k
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS LC-MS LC-MS/MS Alignment
updated 5.4 years ago by ★ 2.1k • written 5.4 years ago by • 0
0
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0
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1.0k
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
6.4 years ago Juliet Hannah ▴ 360
0
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9
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2.7k
views
visualizing alignment without realignment
msa alignment visualization
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
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0
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892
views
Multiple alignment solution for a character object of short fragments
r alignment
6.6 years ago r.tor • 0
0
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9
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3.6k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
6.8 years ago A ▴ 60
0
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0
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1.2k
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
6.8 years ago A ▴ 60
2
votes
1
reply
1.5k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 6.9 years ago by ★ 3.6k • written 6.9 years ago by ▴ 870
0
votes
16
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5.4k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
6.9 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
7.1 years ago ktehmsen • 0
0
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0
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1.5k
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problem for finding relative Version GTF file for my .fa file
alignment BWA Burrows-Wheeler Alignment Tool
7.2 years ago modarzi ▴ 10
1
vote
1
reply
4.2k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 10
1
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2
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2.6k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ▴ 10
0
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4
replies
1.9k
views
Query with Biostrings pairwise alignment output positon
biostrings alignment pairwisealignment
updated 7.8 years ago by 16k • written 7.8 years ago by • 0
2
votes
4
replies
2.8k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.8 years ago by • 0
0
votes
1
reply
1.6k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher alignment
updated 7.9 years ago by ▴ 10 • written 7.9 years ago by • 0
1
vote
4
replies
3.0k
views
How to find the end position of a read?
rsamtools alignment cigar
8.2 years ago Frocha ▴ 20
0
votes
0
replies
1.2k
views
Highlighting only GC mismatches in the Alignment track of Gviz
gviz alignment
8.6 years ago s8shcahk • 0
2
votes
4
replies
1.9k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ★ 1.5k
2
votes
1
reply
2.1k
views
How to remmove duplicated paired end alignments
alignment duplicate
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 20
0
votes
0
replies
1.4k
views
Biostrings "global" alignment does NOT return a global alignment
biostrings alignment
8.9 years ago map2085 ▴ 40
0
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0
replies
1.4k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
8.9 years ago Matthew Thornton ▴ 380
0
votes
16
replies
3.4k
views
Variance between runs of Rsubread
rsubread alignment reproducibility
8.9 years ago Isaac Virshup • 0
0
votes
3
replies
3.7k
views
Is there a package for peptide alignment with protein sequences?
Alignment Alignment
updated 9.1 years ago by • 0 • written 11.9 years ago by ★ 13k
3
votes
4
replies
2.0k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread rnaseq alignment
updated 9.1 years ago by 53k • written 9.1 years ago by • 0
0
votes
4
replies
2.2k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR rnaseq alignment splicemap bowtie2
9.5 years ago Gabriella • 0
0
votes
3
replies
1.9k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap QuasR RNAseq Alignment
updated 9.6 years ago by ▴ 400 • written 9.6 years ago by ▴ 10
0
votes
1
reply
1.8k
views
QuasR: spliced and unspliced alignment
quasr alignment
updated 9.7 years ago by ▴ 400 • written 9.7 years ago by • 0
3
votes
1
reply
1.8k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error rsubread alignment
updated 9.8 years ago by ★ 3.6k • written 9.8 years ago by ▴ 420
208 results • Page 1 of 5
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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It may not be that common for bulk RNA-Seq, but in my experience it's very common for bulk miRNA-Seq.
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Nice. That's great to hear. `sva` was actually the next step I was planning to try. My colleagues haven't seen this kind of pattern before …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by James W. MacDonald 68k
It is not uncommon for library size to be apparent in an MDS plot. You can use `sva` or `RUV` to account for that.
Comment: p-adjusted values in multiple comparisons by Josh • 0
Yes, using lmFit with block and duplicateCorrelation is appropriate; mobile data collection can illustrate blocking importance. First estim…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Understood, thanks. The issue I'm seeing is that even after normalization, the MDSplot still orders samples by library size. I suspect cell…
Votes
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: How to construct a BSgenome object from a custom genome assembly using BSgenomeF
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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