Showing : alignment • reset
0
votes
2
replies
585
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
votes
1
reply
404
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
570
views
Multitasking and Rbwa
Rbwa Alignment
written 11 months ago by • 0
0
votes
2
replies
680
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 11 months ago by ▴ 70
0
votes
0
replies
374
views
Align to reference genome
Alignment
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
0
replies
602
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
14 months ago jsharif • 0
0
votes
0
replies
611
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
16 months ago vonSkopnik • 0
0
votes
1
reply
668
views
Diffenrent result from EMBOSS needle and Biostrings pairwiseAlignment ?
Alignment Biostrings
16 months ago 潘晓光 • 0
0
votes
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
votes
0
replies
685
views
Edit alignment in msa
alig msa Alignment
18 months ago Luis • 0
0
votes
2
replies
826
views
Rsubread align --R session aborts
RNA Alignment Rsubread
20 months ago sreekalasn • 0
0
votes
0
replies
712
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
2.0 years ago saira • 0
0
votes
1
reply
825
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 2.1 years ago by ▴ 380 • written 2.1 years ago by • 0
0
votes
0
replies
644
views
Pairwise alignment results with the original coordinates.
Biostrings Alignment
2.2 years ago Charles Plessy ▴ 180
0
votes
2
replies
984
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
776
views
insufficient alignment
DECIPHER Alignment
3.5 years ago julius_vn • 0
0
votes
2
replies
980
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
743
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
votes
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 6.3 years ago by ▴ 10
0
votes
4
replies
1.3k
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
993
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
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
0
votes
5
replies
1.8k
views
SpliceMap in QuasR package failing when sorting 25mer-alignments
rnaseq quasr alignment
updated 8.4 years ago by ▴ 400 • written 8.4 years ago by • 0
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by marka • 0
As a single dad in Australia, finding time to unwind is rare, but [Lincoln Casino][1] has become my go-to escape after putting the kids to …
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
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Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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