Showing : Alignment • reset
0
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2
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981
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R session aborts after running align function on Rsubread
Rsubread Alignment
updated 19 months ago by ★ 3.6k • written 19 months ago by • 0
0
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1
reply
656
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Generate false reads for testing
mgu74bv2cdf Software Alignment
updated 21 months ago by 68k • written 21 months ago by • 0
0
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3
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933
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Multitasking and Rbwa
Rbwa Alignment
written 22 months ago by • 0
0
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2
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1.1k
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 23 months ago by ▴ 70
0
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0
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549
views
Align to reference genome
Alignment
updated 24 months ago by 68k • written 24 months ago by • 0
0
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0
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911
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.1 years ago agamemnon • 0
0
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0
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939
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
2.2 years ago vonSkopnik • 0
0
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2
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1.1k
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 5 months ago by ▴ 20 • written 2.3 years ago by • 0
0
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1
reply
2.3k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 30
0
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0
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991
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Edit alignment in msa
alig msa Alignment
2.5 years ago Luis • 0
0
votes
2
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1.1k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
2.6 years ago sreekalasn • 0
0
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0
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959
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
3.0 years ago saira • 0
0
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1
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1.1k
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 3.1 years ago by ▴ 450 • written 3.1 years ago by • 0
0
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0
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879
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
3.1 years ago Charles Plessy ▴ 180
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2
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1.3k
views
BLAST-like alignment of a DNAString to a BSgenome?
Alignment Genome
3.4 years ago Charles Plessy ▴ 180
2
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2
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1.8k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 3.7 years ago by 52k • written 3.7 years ago by • 0
0
votes
5
replies
2.0k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 3.8 years ago by ▴ 150 • written 3.9 years ago by ▴ 10
0
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1
reply
1.3k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl Alignment QuasR
updated 4.1 years ago by ▴ 350 • written 4.1 years ago by • 0
0
votes
3
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2.2k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 4.3 years ago by ▴ 450 • written 4.3 years ago by • 0
0
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2
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1.1k
views
insufficient alignment
DECIPHER Alignment
4.4 years ago julius_vn • 0
0
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2
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1.3k
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation Alignment Gviz
4.4 years ago Vaibhav • 0
0
votes
3
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2.2k
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS LC-MS LC-MS/MS Alignment
updated 4.9 years ago by ★ 2.1k • written 4.9 years ago by • 0
0
votes
0
replies
964
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
5.9 years ago Juliet Hannah ▴ 360
1
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1
reply
2.6k
views
Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.9 years ago jcollidelcs • 0
0
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9
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2.4k
views
visualizing alignment without realignment
msa alignment visualization
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
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0
replies
823
views
Multiple alignment solution for a character object of short fragments
r alignment
6.1 years ago r.tor • 0
0
votes
9
replies
3.3k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
6.3 years ago A ▴ 40
0
votes
0
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1.1k
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
6.4 years ago A ▴ 40
2
votes
1
reply
1.4k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 6.4 years ago by ★ 3.6k • written 6.4 years ago by ▴ 870
0
votes
16
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5.0k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
6.4 years ago writetoroopali • 0
0
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0
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1.4k
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM samtools pairwisealignment alignment blastn
6.6 years ago ktehmsen • 0
0
votes
0
replies
1.4k
views
problem for finding relative Version GTF file for my .fa file
alignment BWA Burrows-Wheeler Alignment Tool
6.7 years ago modarzi ▴ 10
1
vote
1
reply
3.8k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 10
1
vote
2
replies
2.3k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 10
0
votes
4
replies
1.8k
views
Query with Biostrings pairwise alignment output positon
biostrings alignment pairwisealignment
updated 7.3 years ago by 16k • written 7.3 years ago by • 0
2
votes
4
replies
2.5k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.3 years ago by • 0
0
votes
1
reply
1.5k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher alignment
updated 7.4 years ago by ▴ 10 • written 7.4 years ago by • 0
1
vote
4
replies
2.8k
views
How to find the end position of a read?
rsamtools alignment cigar
7.7 years ago Frocha ▴ 20
0
votes
0
replies
1.2k
views
Highlighting only GC mismatches in the Alignment track of Gviz
gviz alignment
8.1 years ago s8shcahk • 0
2
votes
4
replies
1.7k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ★ 1.5k
2
votes
1
reply
1.9k
views
How to remmove duplicated paired end alignments
alignment duplicate
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
0
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0
replies
1.4k
views
Biostrings "global" alignment does NOT return a global alignment
biostrings alignment
8.4 years ago map2085 ▴ 40
0
votes
0
replies
1.2k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
8.4 years ago Matthew Thornton ▴ 380
0
votes
16
replies
3.1k
views
Variance between runs of Rsubread
rsubread alignment reproducibility
8.4 years ago Isaac Virshup • 0
3
votes
4
replies
1.9k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread rnaseq alignment
updated 8.7 years ago by 52k • written 8.7 years ago by • 0
0
votes
4
replies
2.0k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR rnaseq alignment splicemap bowtie2
9.0 years ago Gabriella • 0
0
votes
3
replies
1.8k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap QuasR RNAseq Alignment
updated 9.1 years ago by ▴ 400 • written 9.1 years ago by ▴ 10
0
votes
1
reply
1.7k
views
QuasR: spliced and unspliced alignment
quasr alignment
updated 9.2 years ago by ▴ 400 • written 9.2 years ago by • 0
3
votes
1
reply
1.7k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error rsubread alignment
updated 9.3 years ago by ★ 3.6k • written 9.3 years ago by ▴ 420
0
votes
5
replies
2.2k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq quasr alignment
updated 9.3 years ago by ▴ 400 • written 9.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Comment: deseq2 lfc shrinkage with few DEGs by Michael Love 43k
Agree with your edit.
Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) by Michael Love 43k
See above about my recommendation to collaborate with someone familiar with linear models represented in R. I have to limit my time on the …
Votes
Comment: Using TPM from tximport of Salmon output for singscore
Answer: Using TPM from tximport of Salmon output for singscore
Comment: deseq2 lfc shrinkage with few DEGs
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
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