User: tommivat

gravatar for tommivat
tommivat240
Reputation:
240
Status:
Trusted
Location:
Finland
Website:
http://users.ics.tkk.f...
Last seen:
an hour ago
Joined:
6 years, 9 months ago
Email:
t*******@gmail.com

about me

Posts by tommivat

<prev • 19 results • page 1 of 2 • next >
2
votes
1
answer
1.5k
views
1
answers
Answer: A: HUMAnN for metatranscriptomics?
... I think HUMAnN 1.0 does not work for metatranscriptomics but Huttenhower lab is working with something called HUMAnN 2.0 which will work for RNAseq data as well. It will probably be released for public in few months. ...
written 4.3 years ago by tommivat240
1
vote
2
answers
1.4k
views
2
answers
Answer: A: Multidimentional Scaling Analysis
... This is a very common visualization problem, where the most important part is to define a proper similarity function to obtain similarity matrix for your individuals. By quick google, I found this paper which may give you some starting points. After you have generated a similarity matrix (you might ...
written 4.4 years ago by tommivat240
1
vote
4
answers
14k
views
4
answers
Comment: C: How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
... Do you mean, you don't have the bar codes used for different samples at all? In that case, there is not much to do in my understanding. ...
written 4.4 years ago by tommivat240
0
votes
3
answers
1.8k
views
3
answers
Answer: A: Alternative Visualisation Tools To Bar Charts For 16S Sequencing Data
... GraPhlAn is a very nice tool developed in Harvard University School of Public Health. Unfortunately, it does not run online, but it is pretty easy to install and use via Python. ...
written 5.0 years ago by tommivat240
0
votes
2
answers
2.8k
views
2
answers
Comment: C: What Is The Recommended Way To Use Bwa On Files Containing Haplotypes Of An Exom
... Also, this post is from time before BWA mem algoritm so it does not answer to the question of OP in that way. ...
written 5.3 years ago by tommivat240
21
votes
6
answers
6.9k
views
10 follow
6
answers
Problem With Picard Dedup In Illumina Alignment Pipeline
... I'm trying to complement my alignment pipeline with picard dedup as recommended by Broad (see their best practices). I have paired end Illumina reads and I use only reads from chr17 (mapped previsouly) as test data. After, bwa I run picard MarkDuplicates and get the following error Exception in thr ...
picard duplicates alignment written 5.6 years ago by tommivat240 • updated 3.4 years ago by yuanyuan.zhang.cau0
0
votes
1
answer
4.6k
views
1
answers
Comment: C: Nucleotide Substitution Matrix With Iupac Nucleotide Ambiguity Codes
... Thanks for the spot on answer! My task is aligning human normal - tumor fragments. What kind of penalty would you suggest for opening end extending a gap? ...
written 5.7 years ago by tommivat240
8
votes
1
answer
4.6k
views
5 follow
1
answer
Nucleotide Substitution Matrix With Iupac Nucleotide Ambiguity Codes
... I'm looking for a substitution matrix for aligning short DNA sequences using IUPAC nucleotide ambiguity codes. I would guess there are existing solutions but I haven't found any despite of extensive googling. ...
alignment dna written 5.7 years ago by tommivat240 • updated 3 months ago by Biostar ♦♦ 20
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Visualizing Snps In Multiple Samples On A Given Gene
... Thanks Pierre! This is pretty close what I'm looking for. ...
written 6.0 years ago by tommivat240
4
votes
1
answer
2.0k
views
1
answer
Visualizing Snps In Multiple Samples On A Given Gene
... I am working with collections of human exome sequences and developing an interactive UI for browsing interesting SNP (indel and SV) data on samples. My current challenge is to provide per-gene-visualizations for given samples. One purpose of the visualization is to easily provide quick look on how s ...
gene visualization snp written 6.0 years ago by tommivat240 • updated 6.0 years ago by Pierre Lindenbaum117k

Latest awards to tommivat

Appreciated 2.4 years ago, created a post with more than 5 votes. For Variant Filtration By Exclusion Of Common Or Well-Known Variants
Great Question 2.4 years ago, created a question with more than 5,000 views. For Variant Filtration By Exclusion Of Common Or Well-Known Variants
Great Question 2.4 years ago, created a question with more than 5,000 views. For Problem With Picard Dedup In Illumina Alignment Pipeline
Good Question 2.4 years ago, asked a question that was upvoted at least 5 times. For Problem With Picard Dedup In Illumina Alignment Pipeline
Popular Question 2.4 years ago, created a question with more than 1,000 views. For What Are Your Favorite Bioit News Resources / Blogs (2012 Edition)
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Visualizing Snps In Multiple Samples On A Given Gene
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Visualizing Snps In Multiple Samples On A Given Gene
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Cap3 Integration Of Velvet And Newbler Assemblies
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Nucleotide Substitution Matrix With Iupac Nucleotide Ambiguity Codes
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Problem With Picard Dedup In Illumina Alignment Pipeline
Appreciated 4.4 years ago, created a post with more than 5 votes. For Variant Filtration By Exclusion Of Common Or Well-Known Variants
Student 4.6 years ago, asked a question with at least 3 up-votes. For Variant Filtration By Exclusion Of Common Or Well-Known Variants
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Variant Filtration By Exclusion Of Common Or Well-Known Variants
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Problem With Picard Dedup In Illumina Alignment Pipeline
Supporter 5.0 years ago, voted at least 25 times.
Student 6.3 years ago, asked a question with at least 3 up-votes. For Cap3 Integration Of Velvet And Newbler Assemblies
Student 6.8 years ago, asked a question with at least 3 up-votes. For Variant Filtration By Exclusion Of Common Or Well-Known Variants

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1711 users visited in the last hour