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pairwiseAlignment
•
reset
1
vote
2
replies
3.5k
views
Calculate the number of SNP differences between sequences in multiple alignment
pairwisealignment
SNP
dnasequence
7.2 years ago
lordbleys
• 0
4
votes
5
replies
2.6k
views
global alignment in Biostrings , Memory fails when seq. lengths around 50K bp
Biostrings
pairwiseAlignment
updated 9.5 years ago by
Hervé Pagès
16k • written 9.5 years ago by
branislav misovic
▴ 120
0
votes
2
replies
1.6k
views
inconsistent pairwiseAlignment behaviour (Biostrings) with multiple alignments with identical scores
biostrings
pairwisealignment
8.6 years ago
vincent.plagnol
▴ 10
0
votes
3
replies
1.4k
views
How to find multiple overlaps with pairwiseAlignment()?
biostrings
pairwisealignment
updated 6.2 years ago by
Hervé Pagès
16k • written 6.3 years ago by
kgorczak
▴ 10
3
votes
2
replies
1.4k
views
pairwiseAlignments coordinate mapping?
biostrings
pairwisealignment
updated 7.9 years ago by
Hervé Pagès
16k • written 7.9 years ago by
Steve Lianoglou
★ 13k
0
votes
4
replies
1.4k
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 6.4 years ago by
Hervé Pagès
16k • written 6.4 years ago by
dhwani2410
• 0
0
votes
1
reply
1.3k
views
pairwiseAlignment() - Similarity NA% ?
biostrings
pairwisealignment
updated 8.5 years ago by
Hervé Pagès
16k • written 8.5 years ago by
boris.steipe
• 0
2
votes
3
replies
1.2k
views
indels located at the edges of subject and Biostrings pairwiseAlignment function
pairwisealignment
biostrings
8.6 years ago
vincent.plagnol
▴ 10
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
2
votes
1
reply
1.0k
views
Error in score() function on pairwiseAlignment()
biostrings
pairwisealignment
updated 8.0 years ago by
shepherl
3.8k • written 8.0 years ago by
jdydu
• 0
0
votes
0
replies
988
views
Translate to aminoacid, align pairwise and un-translate back to DNA
translation
pairwisealignment
7.7 years ago
igferres
• 0
0
votes
1
reply
867
views
Mapping sequence features to alignments
pairwisealignment
indel
updated 7.8 years ago by
Hervé Pagès
16k • written 7.8 years ago by
oliwindram
▴ 10
12 results • Page
1 of 1
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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