Showing : Alignment • reset
0
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880
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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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979
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 19 months ago by ▴ 70
0
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1
reply
591
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
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868
views
Multitasking and Rbwa
Rbwa Alignment
written 18 months ago by • 0
0
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0
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514
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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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845
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
21 months ago agamemnon • 0
0
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0
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860
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
23 months ago vonSkopnik • 0
0
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2
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979
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
updated 8 weeks ago by ▴ 20 • written 24 months 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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910
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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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892
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
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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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817
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Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.8 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 • updated 3.1 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
1.8k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 3.6 years ago by ▴ 150 • written 3.6 years ago by ▴ 10
0
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1
reply
1.2k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl Alignment QuasR
updated 3.8 years ago by ▴ 350 • written 3.8 years ago by • 0
0
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3
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2.1k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 4.0 years ago by ▴ 450 • written 4.0 years ago by • 0
0
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2
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984
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
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0
replies
899
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
5.6 years ago Juliet Hannah ▴ 360
1
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1
reply
2.4k
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
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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
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792
views
Multiple alignment solution for a character object of short fragments
r alignment
5.8 years ago r.tor • 0
0
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9
replies
3.0k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
6.0 years ago A ▴ 40
0
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0
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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
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4.8k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
6.1 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
6.3 years ago ktehmsen • 0
0
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0
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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 6.6 years ago by 67k • written 6.6 years ago by ▴ 10
1
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2
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2.0k
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
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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 7.1 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
7.8 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
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1.2k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
8.1 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
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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 11.1 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 • updated 8.7 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: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Answer: Feature Counts -R XS Read Assignment Tag by Gordon Smyth 52k
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Comment: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Thanks! This one might be worth remaking with `ComplexHeatmap`. Similar to https://github.com/LieberInstitute/spatialLIBD/pull/91 that was …
Comment: DESeq2 - Comparing Comparisons by James W. MacDonald 67k
Full disclosure: I don't use `DESeq2`, and find the contrasts specification confusing. Because of that, I generally recommend using `result…
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Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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