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align
•
reset
0
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0
replies
341
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
7 months ago
jsharif
• 0
0
votes
0
replies
544
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
17 months ago
saira
• 0
2
votes
2
replies
1.0k
views
Rsubread doesn't output a .bai file
Rsubread
align
Alignment
updated 2.2 years ago by
Gordon Smyth
48k • written 2.2 years ago by
mike_flower
• 0
1
vote
5
replies
1.9k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 3.2 years ago by
James W. MacDonald
63k • written 3.2 years ago by
abano
• 0
0
votes
4
replies
1.0k
views
segfault "memory not mapped" using align from Rsubread
Rsubread
align
3.5 years ago
Joseph Fass
▴ 70
5
votes
6
replies
1.4k
views
Rsubread malloc(): memory corruption
Rsubread
malloc
align
updated 3.9 years ago by
Gordon Smyth
48k • written 4.1 years ago by
Konstantinos Yeles
▴ 80
5
votes
6
replies
1.1k
views
Improving the performance of the align function from Rsubread for old Roche454 reads
align
rsubread
roche454
rnaseq
updated 4.4 years ago by
Wei Shi
★ 3.5k • written 4.4 years ago by
Raito92
▴ 60
0
votes
9
replies
2.0k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
4.8 years ago
A
▴ 40
1
vote
5
replies
1.5k
views
Error using Rsubread align: caugh segfault invalid permissions
rsubread
align
segfault
updated 7.3 years ago by
Wei Shi
★ 3.5k • written 7.3 years ago by
gerard_llimos
▴ 10
0
votes
1
reply
1.5k
views
RSubread 0% mapping
rsubread
mapping
featurecounts
align
7.8 years ago
Jo
▴ 30
10 results • Page
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Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
by
Gordon Smyth
48k
I am telling you that `LS_B.vs.NL_B` is completely uninteresting. You need instead to examine `LS_Y.vs.NL_Y` and `LS_N.vs.NL_N` separately.
Answer: Batch correction and repeated measures
by
Gordon Smyth
48k
You should just do a standard limma analysis as recommended in the previous posts. ``` design <- model.matrix(~0 + Sample.Type + batch) i <…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
• 0
Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…
Votes
Answer: Batch correction and repeated measures
Answer: Batch correction and repeated measures
Answer: Batch correction and repeated measures
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
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