User: Walter F. Baumann
Walter F. Baumann • 10
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Posts by Walter F. Baumann
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... Hi, first of all thanks for moving this discussion. There is a bootstrap mode (--numBootstraps)in salmon and this added information that is needed by wasabi. I set it on 10. The bootstraps are needed to estimate the technical variance in your sample, which is needed by sleuth (and I guess this is wh ...
written 10 months ago by
Walter F. Baumann • 10
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... Hi,
I want to use sleuth on the data salmon returned. In the first step, because sleuth needs actually kallisto, I used wasabi to generate the abundance.h5 file. However, after using
so <- sleuth_prep(s2c, ~ condition, num_cores = 1)
(s2c looks like that: )
sample condition
1 sample1 ...
written 10 months ago by
Walter F. Baumann • 10
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... Hi,
I compared the counts per gene of summarizeOverlaps and HTSeq (python). The correlation was ~0.98. Although the correlation is very good, I was surprised that it was not roughly or equal 1, because summarizeOverlaps is according to the documentation designed after the counting modes in HTSeq ( ...
written 10 months ago by
Walter F. Baumann • 10
• updated 10 months ago by
thokall • 120
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... Hi,
I want to get into Single Cell RNA-Seq and found already a good tutorial (https://www.bioconductor.org/help/workflows/simpleSingleCell/). There a package called SingleCellExperiment is introduced. However, the package does not seem to work for me. I had problems with the installation (it always ...
written 11 months ago by
Walter F. Baumann • 10
• updated 10 months ago by
lahrmannu • 0
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... Hi,
I have to create some GRanges objects, which are located on the + and - strand (The features represent regions on transcripts.). Here a reproducible example:
GRanges(seqnames = Rle(c("chr1", "chr2", "chr3", "chr4")),
ranges = IRanges(10:13, width=3),
strand = Rle(c("+", "-" ...
written 14 months ago by
Walter F. Baumann • 10
• updated 14 months ago by
Michael Lawrence ♦ 10k
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... Hi,
I work with ribosome profiling data and I want to check the coverage of reads on the start codon.
My start is with an GRAngesList object I obtained from cdsBy(txdb, by=„tx).
In the end I want to obtain a GrangesList object with transcript id as names, and start of startcodon and stop of s ...
written 15 months ago by
Walter F. Baumann • 10
• updated 15 months ago by
Hervé Pagès ♦♦ 13k
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Comment:
C: Problems with summarizeOverlaps
... Thanks. I tried to apply the given examples of the Rsamtools and the GenomicAlignments manual on my case, but so far I was not successful. (This is a single-end RNA-Seq experiment).
myalignment <- BamFile(file=„/pathto/Aligned.bam",
index="/pathto/Aligned.bam.bai",
...
written 16 months ago by
Walter F. Baumann • 10
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... Hi,
I want to create a table with counts per region (column), per transcript or gene (row).
First thing I did was to define the regions:
txdb <- makeTxDbFromGFF("/pathto/gencode.v19.annotation.gtf", dataSource="Gencode", organism="Homo sapiens", format="gtf")
txdb_5utr_transcript <- five ...
written 16 months ago by
Walter F. Baumann • 10
• updated 16 months ago by
Martin Morgan ♦♦ 22k
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Answer:
A: DESeq2 Following RSEM
... The DESeq2 manuals says: "As input, the DESeq2 package expects count data as obtained", which means just handles whole numbers. I doubt that "round" is a good approach here, because you change the counts. Where does the e.g. 0.64 count from Sample1 A1BG come from?
...
written 18 months ago by
Walter F. Baumann • 10
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Comment:
C: Error using biocLite
... It should be biocLite("org.Hs.eg.db") (with quotation marks)... However, I just tried it and it works as expected, but I use R 3.3.1.
...
written 18 months ago by
Walter F. Baumann • 10
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