User: Johannes Waage

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50
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New User
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Last seen:
7 years, 1 month ago
Joined:
7 years, 12 months ago
Email:
j*************@bric.dk

Posts by Johannes Waage

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rtracklayer and BED-export
... Dear mailing list, I have a problem with rtraclayer that you can hopefully help me with. I'm trying to export tracks to the UCSC browser or to BED files through rtracklayer, but I have problems with the blockStarts and blockSizes fields functioning, and get a >export(targetTrack, format="bed", ...
written 7.1 years ago by Johannes Waage50 • updated 7.1 years ago by Michael Lawrence9.8k
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Shortread and filtering of duplicate reads
... Hi all, Does anyone know if the shortRead package has functionality to filter out duplicate reads, but only reads with more than n duplicates, to avoid reads stacks caused by PCR-aplification? I can only find srduplicated(), but it doesn't seem to have functionality for specifiying n duplicate read ...
shortread written 7.9 years ago by Johannes Waage50 • updated 7.9 years ago by Martin Morgan ♦♦ 21k
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Answer: A: Get genomic sequences
... Ah, simple but perfect. Thanks! /JW On Mon, Jan 11, 2010 at 11:15 AM, Paul Leo wrote: > If you have a bed file then all you need are the BSgemome.* packages to > get the sequences .... > > library("BSgenome.Mmusculus.UCSC.mm9") > all.genomic<-getSeq(Mmusculus, the.chrom, starts ...
written 7.9 years ago by Johannes Waage50
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Get genomic sequences
... Hi all, Is there a way to fetch genomic sequences via Bioconductor directly? (Using galaxy, but I would like to automate) I tried rtracklayer and biomaRt - rtracklayer doesn't seem to have an interface for fetching sequences, and biomaRt only seems to fetch sequences from a subset of gene ID's, wh ...
biomart rtracklayer written 7.9 years ago by Johannes Waage50 • updated 7.9 years ago by Paul Leo970
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phastCon-scores
... Hi all, I have a small but important challenge set before me, that I've been unable to solve. I need to aggregate all phastCon scores for 75-100 nt around all * mus* exon splicesites. I've tried different approaches, such as downloading the entire mulitz30way phastCon dataset from UCSC (too big to ...
rtracklayer splicesites written 8.0 years ago by Johannes Waage50 • updated 8.0 years ago by Sean Davis21k

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