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pairwiseAlignment
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1.5k
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Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM
samtools
pairwisealignment
alignment
blastn
6.7 years ago
ktehmsen
• 0
0
votes
3
replies
1.8k
views
How to find multiple overlaps with pairwiseAlignment()?
biostrings
pairwisealignment
updated 7.2 years ago by
Hervé Pagès
16k • written 7.2 years ago by
kgorczak
▴ 10
0
votes
4
replies
1.8k
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 7.4 years ago by
Hervé Pagès
16k • written 7.4 years ago by
dhwani2410
• 0
1
vote
2
replies
4.2k
views
Calculate the number of SNP differences between sequences in multiple alignment
pairwisealignment
SNP
dnasequence
8.2 years ago
lordbleys
• 0
0
votes
0
replies
1.3k
views
Translate to aminoacid, align pairwise and un-translate back to DNA
translation
pairwisealignment
8.7 years ago
igferres
• 0
0
votes
1
reply
1.1k
views
Mapping sequence features to alignments
pairwisealignment
indel
updated 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
oliwindram
▴ 10
3
votes
2
replies
1.8k
views
pairwiseAlignments coordinate mapping?
biostrings
pairwisealignment
updated 8.9 years ago by
Hervé Pagès
16k • written 8.9 years ago by
Steve Lianoglou
★ 13k
2
votes
1
reply
1.3k
views
Error in score() function on pairwiseAlignment()
biostrings
pairwisealignment
updated 9.0 years ago by
shepherl
4.1k • written 9.0 years ago by
jdydu
• 0
0
votes
1
reply
1.5k
views
pairwiseAlignment() - Similarity NA% ?
biostrings
pairwisealignment
updated 9.5 years ago by
Hervé Pagès
16k • written 9.5 years ago by
boris.steipe
• 0
2
votes
3
replies
1.4k
views
indels located at the edges of subject and Biostrings pairwiseAlignment function
pairwisealignment
biostrings
9.6 years ago
vincent.plagnol
▴ 10
0
votes
2
replies
2.0k
views
inconsistent pairwiseAlignment behaviour (Biostrings) with multiple alignments with identical scores
biostrings
pairwisealignment
9.6 years ago
vincent.plagnol
▴ 10
4
votes
5
replies
3.2k
views
global alignment in Biostrings , Memory fails when seq. lengths around 50K bp
Biostrings
pairwiseAlignment
updated 10.5 years ago by
Hervé Pagès
16k • written 10.5 years ago by
branislav misovic
▴ 120
12 results • Page
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Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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