User: Daniel.Berner@unibas.ch

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Posts by Daniel.Berner@unibas.ch

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GenomicAlignments/access correct bp positions near indels
... Hi all! My goal is to access the nucleotide content at specific base positions in Illumina reads derived from whole-genome poolseq data, for de novo SNP detection. Alignment to a reference genome is done, so we start with a BAM file. Now one approach I implemented involves reading the BAM into R us ...
snp genomicranges genomicalignments written 7 months ago by Daniel.Berner@unibas.ch90 • updated 7 months ago by Hervé Pagès ♦♦ 13k
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Deleting object rows while looping - III
... Hervé, Steve, Martin Thanks so much for taking the time to make all these valuable suggestions! just by considering Martin's initial hint to work through vectors rather than a data.frame, I managed to speed up the code by 4.2x, and it looks like there is much more potential. Seems I have some homew ...
written 4.6 years ago by Daniel.Berner@unibas.ch90
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Deleting object rows while looping - II
... Martin, Steve Thanks for your suggestions, much appreciated! My core problem is that the operations inside the loop are too complex for me to allow implementing any function() and apply() combination (there are multiple interleaved if() lines etc). and I was not aware of the data.table package, but ...
coverage alignment process written 4.6 years ago by Daniel.Berner@unibas.ch90 • updated 4.6 years ago by Martin Morgan ♦♦ 21k
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Deleting object rows while looping
... Hi Can someone help me with this question: I have a large data frame (say 'dat') with 2 columns, one is genomic loci (chromosome-by-position, e.g. 'chr1_1253454'), the other is Illumina sequences. Now I want to perform some operations on each UNIQUE locus. I thus derive the unique loci: u.loc<-u ...
written 4.6 years ago by Daniel.Berner@unibas.ch90 • updated 4.6 years ago by Martin Morgan ♦♦ 21k
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missing reads in alignerBAM
... hi list When I align the N reads contained in my Illumina fastq using NovoAlign, convert the resulting SAM output to BAM using Samtools, and then upload the BAM file using readAligned (ShortRead), the resulting AlignedRead object contains fewer than N reads. Reconverting the BAM to SAM and counting ...
alignment convert written 7.0 years ago by Daniel.Berner@unibas.ch90 • updated 7.0 years ago by Martin Morgan ♦♦ 21k
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alignment & SNP calling
... Dear list 1) I have illumina short reads from which I want to call SNPs WITHOUT using a reference genome. That is, I want to align the reads among themselves, and then screen each alignment for polymorph positions (SNPs) by taking into account base call quality. Is there a program that would allow b ...
alignment written 7.1 years ago by Daniel.Berner@unibas.ch90 • updated 7.1 years ago by Andreia Fonseca810
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mismatch & replacement
... Hi list 1. I have a large fastq file containing solexa reads that start with a barcode (identifier to separate individuals). I now want to filter that large data set according to the barcodes using ShortRead. I understand that this is easily done with grep() when one wants a perfect barcode match. H ...
shortread written 7.1 years ago by Daniel.Berner@unibas.ch90 • updated 7.1 years ago by Harris A. Jaffee590
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Comment: C: fastq upload time
... thanks, appreciated!! daniel ...
written 7.2 years ago by Daniel.Berner@unibas.ch90
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fastq upload time
... Hi there I have a solexa fastq file containing some 27 million reads (file size approx. 4 GB). my plan is to upload this into R for subsequent editing with ShortRead tools. The R version is 64-bit linux, the computer has 8 GB RAM. Can anybody provide a rough estimate of how long the input will take? ...
shortread written 7.2 years ago by Daniel.Berner@unibas.ch90 • updated 7.2 years ago by Sean Davis21k

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