User: Walter F. Baumann

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Posts by Walter F. Baumann

<prev • 15 results • page 2 of 2 • next >
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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 8 months ago by Walter F. Baumann 10
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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 8 months ago by Walter F. Baumann 10 • updated 8 months ago by Hervé Pagès ♦♦ 13k
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Comparing two RNAseq experiments using summarizeOverlaps
... Hi,  I have two RNA-seq experiments. I first checked them to see whether they are single or pairedEnd using: bamtools view -c -F 1 myfile.bam, bamtools view -c -f 1 myfile2.bam There I saw that all reads are singleEnd. In the next step I uploaded my data in R, and counted the reads per feature by ...
rnaseq R bioconductor summarizeoverlaps rna-seq written 9 months ago by Walter F. Baumann 10 • updated 9 months ago by Hervé Pagès ♦♦ 13k

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