First I create the index using:
buildindex(basename=��Rsubread_index��,reference=��/path/to/hg19.fa",colorspace=FALSE)
Where hg19.fa is the fasta file with the chromosomes, chr1 etc.
Then I run:
align(
index=��/path/to/Rsubread_index��,readfile1=��/path/to/rea
You got to be aware that Rbowtie/bowtie does not detect indels and quite often
this is needed for the analysis of DNA sequencing data. Bowtie is probably the
only aligner that does not detect indels.
As I mentioned in my last email, I would be happy to take a look at why
Rsubread is slow if you
It would seem to be a bug in endoapply
lst <- SimpleList(
m = matrix(0, 2, 2, dimnames=list(letters[1:2], LETTERS[1:2])),
df = data.frame(A=1:2, B=1:2, row.names=letters[1:2])
)
dimnames(lst[[1]]) # list(c("a", "b"), c("A", "B"))
dimnames(endoapply(lst, identity)[[1]]
Confirmed with the following sessionInfo(), satisfying biocValid()==TRUE
> sessionInfo()
R Under development (unstable) (2017-11-22 r73776)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.1
Matrix products: default
BLAS: /home/stvjc/R-35-dist/lib/R/lib/libRblas.so
LAPACK
Hi all,
I got different results constructing a SummarizedExperiment in 3.6 and 3.7. My
question is, whether this is intentional or a bug.
library(GenomicRanges)
library(SummarizedExperiment)
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
colnames(counts) <- LETTE
I used Rbowtie and the mapping was done in 7 minutes, the results where fine
too. Rsubread had been running for 2 days so I had to stop it.
But anyway I can use Rbowtie which is nice :)
Ioannis Vardaxis
Stipendiat NTNU
Sendt fra min iPhone
26. nov. 2017 kl. 04:14 skrev Martin Morgan
mailto:mar
Thanks Martin.
Ioannis: could you please provide your command and screen output from the
mapping so I can try to see what might cause the long running time?
Thanks,
Wei
From: Martin Morgan
Sent: Sunday, November 26, 2017 2:13:43 PM
To: Ioannis Vardaxis; A.E.S.;
