Moderator: matted
matted ♦ 6.5k
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Posts by matted
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2.6k
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... [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 15 months ago by
matted ♦ 6.5k
1
vote
6
answers
965
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6
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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 17 months ago by
matted ♦ 6.5k
2
votes
6
answers
965
views
6
answers
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 17 months ago by
matted ♦ 6.5k
0
votes
1
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594
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1
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... You may want to check out this interesting recent paper:
"Genetic Variation in Human DNA Replication Timing" Cell (2014)
They used variation in read coverage from whole-genome sequencing in the 1000 Genomes Project to infer replication origin locations. After that, they found replication origin d ...
written 19 months ago by
matted ♦ 6.5k
1
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1
answer
520
views
1
answers
... Yes, that all sounds right to me.
...
written 19 months ago by
matted ♦ 6.5k
4
votes
1
answer
463
views
1
answers
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 ex ...
written 19 months ago by
matted ♦ 6.5k
2
votes
1
answer
520
views
1
answers
... 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 normalizat ...
written 19 months ago by
matted ♦ 6.5k
4
votes
1
answer
770
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1
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... 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 19 months ago by
matted ♦ 6.5k
2
votes
1
answer
629
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1
answers
... 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 19 months ago by
matted ♦ 6.5k
2
votes
2
answers
818
views
2
answers
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 19 months ago by
matted ♦ 6.5k
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