User: Nora Rieber

gravatar for Nora Rieber
Nora Rieber40
Reputation:
40
Status:
New User
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Last seen:
7 years, 10 months ago
Joined:
8 years, 2 months ago
Email:
n*******@dkfz-heidelberg.de

Posts by Nora Rieber

<prev • 4 results • page 1 of 1 • next >
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extendReads in package chipseq - reads are extended below zero
... Dear all, has anybody noticed that extendReads() seems to extend reads on the minus strand below zero? For example, if I have a 36 nt read starting at base 215 on the minus strand, and use extendReads(aln, seqLen=350), aln being an object of class AlignedRead, my resulting extended read runs from b ...
written 7.9 years ago by Nora Rieber40
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"islands" and number of reads in the island in package chipseq/ShortRead
... Dear all, I'm looking for a fast way of computing how many reads map into a certain location (e.g. between position 300 and 400 on chromosome 14). Is there any function to compute this in the packages chipseq or ShortRead? After reading the vignette for chipseq, I thought viewSums(islands) compute ...
chipseq coverage written 8.0 years ago by Nora Rieber40 • updated 8.0 years ago by Kasper Daniel Hansen6.3k
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possible bug in extendReads() in package chipseq
... Dear all, I'm using the ShortRead package to read in my MAQ alignment output files with readAligned. Then I extract a subset of reads mapping to one chromosome: aln_Pat_chr<-aln_Pat[chromosome(aln_Pat)==chromosomeString] and extend the reads with extendReads: aln_Pat_chr_extended<-extendR ...
alignment shortread written 8.1 years ago by Nora Rieber40 • updated 8.1 years ago by Martin Morgan ♦♦ 21k
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pileup function in ShortRead package
... Hi there, I'm using the pileup function in the ShortRead package and it seems I call it with the wrong arguments, or that there is some kind of bug in the function. All my reads are piled up in forward direction only, even if they were actually mapped to the backward strand. Here's a small (nonfun ...
alignment shortread written 8.2 years ago by Nora Rieber40 • updated 8.2 years ago by Martin Morgan ♦♦ 21k

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