Showing : Alignment • reset
0
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2
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591
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
0
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2
replies
685
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 12 months ago by ▴ 70
0
votes
1
reply
406
views
Generate false reads for testing
mgu74bv2cdf Software Alignment
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
3
replies
573
views
Multitasking and Rbwa
Rbwa Alignment
written 11 months ago by • 0
0
votes
0
replies
378
views
Align to reference genome
Alignment
updated 13 months ago by 65k • written 13 months ago by • 0
0
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0
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606
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
14 months ago jsharif • 0
0
votes
0
replies
614
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
16 months ago vonSkopnik • 0
0
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1
reply
671
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
16 months ago 潘晓光 • 0
0
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1
reply
1.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 17 months ago by 65k • written 17 months ago by ▴ 30
0
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0
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685
views
Edit alignment in msa
alig msa Alignment
18 months ago Luis • 0
0
votes
2
replies
828
views
Rsubread align --R session aborts
RNA Alignment Rsubread
21 months ago • updated 20 months ago sreekalasn • 0
0
votes
0
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713
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
2.1 years ago saira • 0
0
votes
1
reply
827
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 2.1 years ago by ▴ 380 • written 2.2 years ago by • 0
0
votes
0
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648
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.2 years ago Charles Plessy ▴ 180
0
votes
2
replies
987
views
BLAST-like alignment of a DNAString to a BSgenome?
Alignment Genome
2.5 years ago Charles Plessy ▴ 180
2
votes
2
replies
1.3k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 2.8 years ago by 50k • written 2.8 years ago by • 0
0
votes
5
replies
1.4k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 2.9 years ago by ▴ 150 • written 3.0 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Error when running qAlign from QuasR package for sequence alignment & QC.
QualityControl Alignment QuasR
updated 3.2 years ago by ▴ 350 • written 3.2 years ago by • 0
0
votes
3
replies
1.7k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 3.4 years ago by ▴ 380 • written 3.4 years ago by • 0
0
votes
2
replies
778
views
insufficient alignment
DECIPHER Alignment
3.5 years ago julius_vn • 0
0
votes
2
replies
984
views
Can we align all the names of the transcripts (GeneRegionTrack) in the plotTracks() output?
Annotation Alignment Gviz
3.5 years ago Vaibhav • 0
0
votes
3
replies
1.4k
views
Merging and Aligning LC-MS/MS Data With XCMS (multiple scan ranges/polarities)
XCMS LC-MS LC-MS/MS Alignment
updated 4.0 years ago by ★ 2.0k • written 4.0 years ago by • 0
0
votes
0
replies
744
views
concatenating a proteome to use Biostrings pairwiseAlignment
Biostrings alignment
5.0 years ago Juliet Hannah ▴ 360
1
vote
1
reply
2.0k
views
Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.0 years ago jcollidelcs • 0
0
votes
9
replies
1.9k
views
visualizing alignment without realignment
msa alignment visualization
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
0
votes
0
replies
692
views
Multiple alignment solution for a character object of short fragments
r alignment
5.2 years ago r.tor • 0
0
votes
9
replies
2.6k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread alignment align
5.4 years ago A ▴ 40
0
votes
0
replies
872
views
Quantifying reporter expression to validate sequencing
alignment Fastq fasta
5.4 years ago A ▴ 40
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 850
0
votes
16
replies
4.3k
views
Error while using buildindex for human genome
rsubread buildindex fasta alignment
5.5 years ago writetoroopali • 0
0
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0
replies
1.1k
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM samtools pairwisealignment alignment blastn
5.7 years ago ktehmsen • 0
0
votes
0
replies
1.1k
views
problem for finding relative Version GTF file for my .fa file
alignment BWA Burrows-Wheeler Alignment Tool
5.8 years ago modarzi ▴ 10
1
vote
1
reply
2.7k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
1
vote
2
replies
1.7k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 6.3 years ago by ★ 28k • written 6.4 years ago by ▴ 10
0
votes
4
replies
1.4k
views
Query with Biostrings pairwise alignment output positon
biostrings alignment pairwisealignment
updated 6.4 years ago by 16k • written 6.4 years ago by • 0
2
votes
4
replies
2.1k
views
running msa (msa) aborts R session
msa alignment r software error
written 6.4 years ago by • 0
0
votes
1
reply
1.2k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher alignment
updated 6.5 years ago by ▴ 10 • written 6.5 years ago by • 0
1
vote
4
replies
2.2k
views
How to find the end position of a read?
rsamtools alignment cigar
6.8 years ago Frocha ▴ 20
0
votes
0
replies
994
views
Highlighting only GC mismatches in the Alignment track of Gviz
gviz alignment
7.2 years ago s8shcahk • 0
2
votes
4
replies
1.3k
views
plotting proteases digestion points in a protein
biostrings iranges sequence alignment protein
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ★ 1.5k
2
votes
1
reply
1.4k
views
How to remmove duplicated paired end alignments
alignment duplicate
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Biostrings "global" alignment does NOT return a global alignment
biostrings alignment
7.5 years ago map2085 ▴ 40
0
votes
0
replies
1.1k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
7.5 years ago Matthew Thornton ▴ 350
0
votes
16
replies
2.5k
views
Variance between runs of Rsubread
rsubread alignment reproducibility
7.5 years ago Isaac Virshup • 0
0
votes
3
replies
3.1k
views
Is there a package for peptide alignment with protein sequences?
Alignment Alignment
updated 7.7 years ago by • 0 • written 10.5 years ago by ★ 13k
3
votes
4
replies
1.5k
views
Error message when trying to use the 'Align' function of the 'Rsubread' package
rsubread rnaseq alignment
updated 7.8 years ago by 50k • written 7.8 years ago by • 0
0
votes
4
replies
1.7k
views
Splicemap (in QuasR) failed while aligning 25mers
QuasR rnaseq alignment splicemap bowtie2
8.1 years ago Gabriella • 0
0
votes
3
replies
1.5k
views
RNAseq_alignment_SpliceMap processing time_QuasR
SpliceMap QuasR RNAseq Alignment
updated 8.2 years ago by ▴ 400 • written 8.2 years ago by ▴ 10
0
votes
1
reply
1.4k
views
QuasR: spliced and unspliced alignment
quasr alignment
updated 8.3 years ago by ▴ 400 • written 8.3 years ago by • 0
3
votes
1
reply
1.5k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error rsubread alignment
updated 8.4 years ago by ★ 3.6k • written 8.4 years ago by ▴ 420
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Votes
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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