User: tomas.bjorklund

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20
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New User
Location:
Sweden
Last seen:
4 years, 7 months ago
Joined:
4 years, 11 months ago
Email:
t**************@med.lu.se

Posts by tomas.bjorklund

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Comment: C: convert GAlignmentPairs to GAlignment
... Another update.... pandaseq-sam (https://github.com/neufeld/pandaseq-sam) could also have been an alternative. However, the algoritm it uses to generate the merged sequence is unclear and the output is only a FASTA that then needs to be aligned again with bowtie, but now all read quality information ...
written 4.6 years ago by tomas.bjorklund20
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Comment: C: convert GAlignmentPairs to GAlignment
... As an update to this, I can say that I'm now testing to approaches, but neither of them is 100% what I would like. The first one is that I use the FLASH utility to first merge any overlapping paired end reads and then align them using bowtie2. The other alternative I use is the "clipOverlap" functio ...
written 4.6 years ago by tomas.bjorklund20
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Comment: C: convert GAlignmentPairs to GAlignment
... Hi Hervé, Thank you for your very helpful reply. Yes, the granges() function is what I use today and for many use cases this is perfectly acceptable. For the application I'm after, however, I'm trying to incorporate annotation of mutations into the sequence as well. We use gene chip arrays to produ ...
written 4.6 years ago by tomas.bjorklund20
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convert GAlignmentPairs to GAlignment
... I'm building a workflow in biconductor to evaluate in vivo viral vector function with assessment using paired-end illumina sequencing. In this workflow, I'm aligning the paired reads to a known genomic reference from which all the vector genomes are derived although all with different regions of the ...
ripseeker galignmentpairs galp2gal written 4.6 years ago by tomas.bjorklund20
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Extract the optimized DNA sequence from a GeneGA instance
... I'm using the GeneGA package to optimize the codon utilization and secondary structure of a large list of DNA sequences. The program works as expected, but I have issues figuring out the GeneGA instance generated and the documentation is very sparse.... if I pipe the output of GeneGA to a GeneGA.res ...
genega written 4.9 years ago by tomas.bjorklund20
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Answer: A: GeneGA organism abbreviations
... For anyone else who is interested, I injected the human CAI information in the wSet data table and then saved it into a new .rda file and replaced the one in the GeneGA data folder. This appears now to work well. Not the most elegant solution long term. In parallel, I have contacted the GeneGA packa ...
written 4.9 years ago by tomas.bjorklund20
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Comment: C: GeneGA organism abbreviations
... Thank you Vincent. This is clearly one step forward and two steps back as the list contains no mammalian species. I have the equivalent data for the species I need however. Is there a way to inject this data into the wSet data table before execution or make it always include this data as it has done ...
written 4.9 years ago by tomas.bjorklund20
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Answer: A: Interpretation of GeneGA results
... Hi Maciej, Can I ask you how you managed to specify maize as the organism? I cannot get any abbreviation to work but the default "ec" I totally agree that the documentation for this package is really lacking. That is unfortunate, as there are no good alternatives in R or as command line tools, as ...
written 4.9 years ago by tomas.bjorklund20
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GeneGA organism abbreviations
... I'm trying to use GeneGA as a component in codon optimisation for expression of polypeptide sequences in mammalian cells. It appears to work well, but I have an annoying issue. The package is said to include a database to optimise for 200 organisms. However, the abbreviation used to specify which or ...
genega written 4.9 years ago by tomas.bjorklund20
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Answer: A: How to reverse translate amino acid sequence into mammalian codon optimised cDNA
... Hi again, It seems like the second part, the codon optimisation, maybe could be achieved by GeneGA in Bioconductor. Is someone familiar with this and could recommend it? ...
written 4.9 years ago by tomas.bjorklund20

Latest awards to tomas.bjorklund

Popular Question 4.6 years ago, created a question with more than 1,000 views. For convert GAlignmentPairs to GAlignment
Popular Question 4.6 years ago, created a question with more than 1,000 views. For How to reverse translate amino acid sequence into mammalian codon optimised cDNA

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