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BWA
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reset
2
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4
replies
3.0k
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isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa
Rsamtools
3.9 years ago
sbcn
▴ 80
0
votes
0
replies
1.4k
views
problem for finding relative Version GTF file for my .fa file
alignment
BWA
Burrows-Wheeler Alignment Tool
6.6 years ago
modarzi
▴ 10
1
vote
11
replies
3.1k
views
rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
rsubread
BWA
NGS
updated 8.4 years ago by
Wei Shi
★ 3.6k • written 8.5 years ago by
tarek.mohamed
▴ 10
1
vote
1
reply
1.7k
views
MeDIPS and use of the 'bwa' parameter
R
medip-seq
medips
bwa
updated 8.5 years ago by
Lukas Chavez
▴ 570 • written 8.5 years ago by
stb
• 0
0
votes
5
replies
5.1k
views
bioconductor package for BWA-MEM ?
bwa
ngs
updated 9.5 years ago by
Gordon Smyth
52k • written 9.5 years ago by
KB
▴ 50
5 results • Page
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Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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Jim Nemesh
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Hervé Pagès
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