User: Walter F. Baumann

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Posts by Walter F. Baumann

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Width in IRanges objects on "+" and "-" strand
... 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("+", "-" ...
iranges granges grangeslist written 5 weeks ago by Walter F. Baumann 0 • updated 5 weeks ago by Michael Lawrence9.4k
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Extracting Coordinates of startcodon from Grangeslist
... 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 ...
biomart grangeslist bioconductor ribosome profiling cds written 12 weeks ago by Walter F. Baumann 0 • updated 12 weeks ago by Hervé Pagès ♦♦ 12k
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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 12 weeks ago by Walter F. Baumann 0
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Problems with summarizeOverlaps
... 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 ...
rnaseq bioconductor summarizeoverlaps written 3 months ago by Walter F. Baumann 0 • updated 3 months ago by Martin Morgan ♦♦ 20k
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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 5 months ago by Walter F. Baumann 0
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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 5 months ago by Walter F. Baumann 0
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Finding candidate binding sites for RNA binding proteins in R
...   Hi, I need to scan mRNAs for binding motifs of RBPs (RNA binding proteins) in human.  After some research I came across this tutorial on how to find candidate binding sites of known transcription factors. So far I did not saw an implemented tool to directly work with RNA or RBPs. I downloaded ...
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Comment: C: Troubles with new version of GenomicFeatures(?)
... Thank you for the useful link, but it unfortunately did not solve my problem. I reinstalled the dependencies of GenomicFeatures: biocLite(c("BiocGenerics", "S4Vectors", "IRanges", "GenomeInfoDb", "GenomicRanges", "AnnotationDbi", "GenomicFeatures")) I use the same versions of packages on my other ...
written 5 months ago by Walter F. Baumann 0
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Troubles with new version of GenomicFeatures(?)
... Hi, I have the following command which always worked well, until now.      txdb <- makeTxDbFromGFF("/path/to/gencode.v19.annotation.gtf", dataSource="Gencode", organism="Homo sapiens", format="gtf") Now I get the following output:      Import genomic features from the file as a GRanges object ...
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summarizeOverlaps counting exons and 5UTR reads
... Hey, I try to compare counts from 2 RNA seq data. I am interested in the 5'UTR and want to compare this number with the total number of reads per transcript. Here my code:      txdb is the gtf file from Gencode (v19) "Comprehensive gene annotation"      txdb_5utr_transcript <- fiveUTRsByTransc ...
rnaseq summarizeoverlaps written 5 months ago by Walter F. Baumann 0 • updated 5 months ago by Hervé Pagès ♦♦ 12k

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