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Moderator: matted

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matted ♦ 7.3k
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Posts by matted

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Answer: A: How to tell bloodtype from SNPs data?
... [Promethease][1] should work for this. They have an [example report][2] from Ancestry.com data that includes a blood type prediction (click the "Blood" tab). There are many related web tools in this space; see http://www.23andyou.com/3rdparty for one list. [1]: https://promethease.com/ [2]: h ...
written 4.6 years ago by matted ♦ 7.3k
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Comment: C: FASTA file of fixed length
... I would've preferred to give an answer using [seqtk][1], but I couldn't find an option for absolute trimming. [1]: https://github.com/lh3/seqtk ...
written 4.8 years ago by matted ♦ 7.3k
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Answer: A: FASTA file of fixed length
... Why reinvent the wheel? Install [FASTX-toolkit][1] and run: fasta_formatter -i input.fa | fastx_trimmer -l 45 > output.fa [1]: http://hannonlab.cshl.edu/fastx_toolkit/ ...
written 4.8 years ago by matted ♦ 7.3k
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Answer: A: What are some of the state of the art approaches for prediction of origins of re
... You may want to check out this interesting recent paper: ["Genetic Variation in Human DNA Replication Timing"](http://www.cell.com/cell/abstract/S0092-8674(14)01313-0) Cell (2014) They used variation in read coverage from whole-genome sequencing in the 1000 Genomes Project to infer replication ori ...
written 4.9 years ago by matted ♦ 7.3k • updated 2.4 years ago by _r_am ♦ 32k
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Comment: C: What kind of systematic bias of sequencing data the following normalization proc
... Yes, that all sounds right to me. ...
written 4.9 years ago by matted ♦ 7.3k • updated 2.4 years ago by _r_am ♦ 32k
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Answer: A: Question on alignment
... It sounds like you want semi-global alignment (also known as "glocal"). You have to align all of A against a portion of B, so global isn't right (all of A against all of B) and local isn't right (some of A against some of B). The algorithm is a hybrid of global and local alignment, as you might exp ...
written 4.9 years ago by matted ♦ 7.3k • updated 2.4 years ago by _r_am ♦ 32k
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Answer: A: What kind of systematic bias of sequencing data the following normalization proc
... I don't know anything about this particular approach, but here's a guess: Imagine the total sequencing depths were different for tumor and normal. This would give you a multiplicative factor inside the log, which is additive once you take it outside the log. So this procedure (additive normalizatio ...
written 4.9 years ago by matted ♦ 7.3k • updated 2.4 years ago by _r_am ♦ 32k
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Answer: A: Is it possible to extract the reference sequence from the BWA index files?
... This is an interesting question.  It definitely should be possible, so I guess the question may be how to do it with existing tools and the least amount of pain. I looked into it, and it seems that from the original bwtsw code (that bwa relies on, particularly for the indexing steps), the "packed" ...
written 4.9 years ago by matted ♦ 7.3k
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Answer: A: Significant of LASSO regression parameters
... This is an active area of recent research and isn't as straightforward as plain linear regression.  See this paper for one approach: "A significance test for the lasso". ...
written 5.0 years ago by matted ♦ 7.3k
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Answer: A: Ion Torrent sample data
... This may not get you everything that you want, but it could be a start. DNAnexus has an SRA search engine (sra.dnanexus.com) where you can filter by instrument type.  Using it, I see 683 studies from Ion PGM or Proton machines, 29 of which are human samples.  Going through some of these may lead yo ...
written 5.0 years ago by matted ♦ 7.3k

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