Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

Moderator: matted

gravatar for matted
matted ♦ 7.0k
Reputation:
7,010
Status:
Trusted
Location:
Boston, United States
Website:
http://www.mdedwards.org/
Scholar ID:
Google Scholar Page
Last seen:
2 years, 4 months ago
Joined:
6 years, 9 months ago
Email:
m*******@gmail.com

Posts by matted

<prev • 343 results • page 1 of 35 • next >
3
votes
1
answer
8.1k
views
1
answers
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 2.7 years ago by matted ♦ 7.0k
1
vote
6
answers
2.2k
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 2.9 years ago by matted ♦ 7.0k
2
votes
6
answers
2.2k
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 3.0 years ago by matted ♦ 7.0k
0
votes
1
answer
944
views
1
answers
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 3.1 years ago by matted ♦ 7.0k • updated 6 months ago by RamRS ♦ 20k
1
vote
1
answer
921
views
1
answers
Comment: C: What kind of systematic bias of sequencing data the following normalization proc
... Yes, that all sounds right to me. ...
written 3.1 years ago by matted ♦ 7.0k • updated 6 months ago by RamRS ♦ 20k
4
votes
1
answer
801
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 ...
written 3.1 years ago by matted ♦ 7.0k • updated 6 months ago by RamRS ♦ 20k
2
votes
1
answer
921
views
1
answers
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 3.1 years ago by matted ♦ 7.0k • updated 6 months ago by RamRS ♦ 20k
6
votes
1
answer
1.6k
views
1
answers
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 3.1 years ago by matted ♦ 7.0k
3
votes
1
answer
1.1k
views
1
answers
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 3.1 years ago by matted ♦ 7.0k
2
votes
2
answers
1.7k
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 3.1 years ago by matted ♦ 7.0k

Latest awards to matted

Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Scholar 2.7 years ago, created an answer that has been accepted. For A: Where can i find some bacterial RNA-Seq data?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Scholar 3.0 years ago, created an answer that has been accepted. For A: Where can i find some bacterial RNA-Seq data?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Scholar 3.0 years ago, created an answer that has been accepted. For A: Where can i find some bacterial RNA-Seq data?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Where can i find some bacterial RNA-Seq data?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Scholar 3.1 years ago, created an answer that has been accepted. For A: Where can i find some bacterial RNA-Seq data?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Where can i find some bacterial RNA-Seq data?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Programming Challenge - Synthetic Whole Genome Vcf
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Programming Challenge - Synthetic Whole Genome Vcf
Appreciated 3.5 years ago, created a post with more than 5 votes. For C: Install Samtools On Suse Linux
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: S. Cerevisiae Synthetic Lethal Database
Scholar 3.5 years ago, created an answer that has been accepted. For A: Where can i find some bacterial RNA-Seq data?
Appreciated 3.6 years ago, created a post with more than 5 votes. For C: Install Samtools On Suse Linux
Appreciated 3.6 years ago, created a post with more than 5 votes. For C: Install Samtools On Suse Linux
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Changing Quality Scores Within Bam Files
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Programming Challenge - Synthetic Whole Genome Vcf
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1975 users visited in the last hour