Moderator: matted
matted ♦ 7.2k
- Reputation:
- 7,160
- Status:
- Trusted
- Location:
- Boston, United States
- Website:
- http://www.mdedwards.org/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 years ago
- Joined:
- 7 years, 4 months ago
- Email:
- m*******@gmail.com
Posts by matted
<prev
• 343 results •
page 1 of 35 •
next >
3
votes
1
answer
9.6k
views
1
answers
... [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 3.4 years ago by
matted ♦ 7.2k
1
vote
6
answers
2.8k
views
6
answers
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 3.6 years ago by
matted ♦ 7.2k
2
votes
6
answers
2.8k
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 3.6 years ago by
matted ♦ 7.2k
0
votes
1
answer
1.0k
views
1
answers
... 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 ...
1
vote
1
answer
1.1k
views
1
answers
... Yes, that all sounds right to me. ...
4
votes
1
answer
890
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 exp ...
2
votes
1
answer
1.1k
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 normalizatio ...
6
votes
1
answer
1.8k
views
1
answers
... 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 3.7 years ago by
matted ♦ 7.2k
3
votes
1
answer
1.3k
views
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 3.8 years ago by
matted ♦ 7.2k
2
votes
2
answers
2.1k
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 3.8 years ago by
matted ♦ 7.2k
Latest awards to matted
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Scholar
3.4 years ago,
created an answer that has been accepted.
For A: Where can i find some bacterial RNA-Seq data?
Teacher
3.5 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Scholar
3.6 years ago,
created an answer that has been accepted.
For A: Where can i find some bacterial RNA-Seq data?
Teacher
3.6 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Scholar
3.6 years ago,
created an answer that has been accepted.
For A: Where can i find some bacterial RNA-Seq data?
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: Where can i find some bacterial RNA-Seq data?
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: Where can i find some bacterial RNA-Seq data?
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: Where can i find some bacterial RNA-Seq data?
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Teacher
3.8 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Good Answer
3.9 years ago,
created an answer that was upvoted at least 5 times.
For A: Programming Challenge - Synthetic Whole Genome Vcf
Teacher
4.1 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Good Answer
4.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Programming Challenge - Synthetic Whole Genome Vcf
Appreciated
4.1 years ago,
created a post with more than 5 votes.
For C: Install Samtools On Suse Linux
Teacher
4.1 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: S. Cerevisiae Synthetic Lethal Database
Scholar
4.2 years ago,
created an answer that has been accepted.
For A: Where can i find some bacterial RNA-Seq data?
Appreciated
4.3 years ago,
created a post with more than 5 votes.
For C: Install Samtools On Suse Linux
Appreciated
4.3 years ago,
created a post with more than 5 votes.
For C: Install Samtools On Suse Linux
Popular Question
4.3 years ago,
created a question with more than 1,000 views.
For Changing Quality Scores Within Bam Files
Good Answer
4.3 years ago,
created an answer that was upvoted at least 5 times.
For A: Programming Challenge - Synthetic Whole Genome Vcf
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1507 users visited in the last hour