Moderator: Damian Kao
Damian Kao ♦ 14k
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Post-doctoral bioinformatician at University of Oxford
Posts by Damian Kao
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... Repeatmasker is used here to prevent augustus from predicting genes in repeat regions. ...
written 10 weeks ago by
Damian Kao ♦ 14k
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... K-mer spectra of genomic reads are usually modeled as a poisson mixture process where each of the components represents the variety of ploidies of a genome. So a k-mer spectra that looks like the following can be interpreted as showing a poisson component representing heterozygous regions (1N) and a ...
written 10 weeks ago by
Damian Kao ♦ 14k
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... I agree with you to a degree about the Q&A format. I think a nicely structured searchable knowledge base would be very helpful and maybe SE can become that.
But I also think that the nature of the bioinformatics field probably means there are enough questions of the abstract type which warrant ...
written 11 weeks ago by
Damian Kao ♦ 14k
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... I think the main problem people have with BioStar boils down to an identity crisis. Is BioStar a Q and A site or a forum?
A Q and A type site requires the question to be technical and precise. If someone asks how to convert a format to another format, that can be easily answered.
But if someone ...
written 3 months ago by
Damian Kao ♦ 14k
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... I completely agree with this. I started my phd as the only bioinformatics student in a molecular lab. Biostars was extremely helpful in not just in answering my questions, but also in expanding my knowledge. I learned tons from reading questions/answers that have no relevance to my phd. I don't see ...
written 3 months ago by
Damian Kao ♦ 14k
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Comment:
C: Abyss path subprograms
... Thanks for the reply. So the k parameter essentially just let's you specify how long of an overlap you want to consider in building the graph. In the case of AdjList, I guess I'll just set it the same as the -m parameter.
So far all the down-stream programs I've tried are working with the SGA unit ...
written 3 months ago by
Damian Kao ♦ 14k
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... How is the k-mer length used after the initial unitig step in Abyss? Isn't the k-mer length only really relevant in the debruijn unitig assembly step? I want to input unitigs that I generated from SGA and use them for the downstream Abyss steps (AdjList, filtergraph, MergeContigs, etc).
Specificall ...
written 3 months ago by
Damian Kao ♦ 14k
• updated
3 months ago by
benv • 500
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... The error sounds like there is a string somewhere in your files (bedgraph or genome file) where there is supposed to be a integer. Try grepping for "size" in either files. ...
written 5 months ago by
Damian Kao ♦ 14k
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... Nice. I think this is how miniasm does it's alignments also? ...
written 5 months ago by
Damian Kao ♦ 14k
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... You are writing it as a binary file ('wb'). Is that what you wanted to do? If you want to open it as text, just use 'w' instead of 'wb'. ...
written 6 months ago by
Damian Kao ♦ 14k
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For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
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For A: Deseq Sizefactors Help
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For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
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For Converting Solid To Srf
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For contigs and scaffolds in abyss
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For A Chat With Oxford Nanopore’S Clive Brown At Agbt 2013
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