Moderator: David Langenberger

Reputation:
8,670
Status:
Trusted
Location:
Deutschland
Website:
http://www.ecseq.com/
Twitter:
ecSeq
Scholar ID:
Google Scholar Page
Last seen:
2 days, 22 hours ago
Joined:
7 years ago
Email:
d*****************@ecseq.com

Bioinformatician with focus on computational and statistical analysis of sequencing data.

- PhD in Bioinformatics with focus on small non-coding RNAs and high-throughput sequencing 
- 10 years of programming experience (Perl, C, R)
- Experience in statistical and automated analysis of big datasets
- strong scientific publication record

Specialties: next-generation sequencing, transcriptomics, small non-coding RNAs, training, consulting, networking


Posts by David Langenberger

<prev • 495 results • page 1 of 50 • next >
2
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... I think there is a difference between using tophat to detect some very special splice sites in very special cases (and probably loosing a lot of others) and tophat being still one of the most cited tool (with knowing that all these people using it will most likely loose a lot of splice sites). ...
written 24 days ago by David Langenberger8.7k
0
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... STAR looks similar and Tophat2 not so good. Now I'm curious about Tophat2, too. :) ...
written 26 days ago by David Langenberger8.7k
2
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... The point with the different languages and platforms is a good one. I always think everyone is using Linux, but obviously for quite a number a Windows solution is of interest. We should add this information to our next update. And also the exact calls of the tools we compared. It should be directl ...
written 26 days ago by David Langenberger8.7k
3
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... 1. You have to follow the links. :) If you click on the ‚here‘ of ‘Please find more information in the benchmark details here.’, you will be forwarded to another page and at the bottom of this is a link to the proceedings. There is everything then: scripts, calls, datasets, etc. 2. Sometimes you n ...
written 26 days ago by David Langenberger8.7k • updated 13 days ago by RamRS20k
2
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... I think there is no perfect benchmark possible. And all tools mentioned are really good. We use all of them during courses and/or in-house. And, of course, you’re absolutely right: the discussions here are awesome and always very fruitful. But that’s due to the fact that this forum is full of high ...
written 26 days ago by David Langenberger8.7k
2
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... And the discussion with n=1 we already had. I see your point. :) But still, all scripts and calls are given. We really really encourage all curious researchers to do the benchmarking themselves, since you really start to understand these mapping tools, when you do that. Based on experience, most non ...
written 26 days ago by David Langenberger8.7k
2
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... I completely see your point, but sometimes it is of high interest to detect the 2% which can not be found by some mappers. 2% of some billion reads is actually quite a number. And in these cases, I would go for a special mapping tool? So, I think it is important to highlight these minor differences ...
written 26 days ago by David Langenberger8.7k
2
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... 1. If you follow the links, you find the exact parameters for every single tool. 2. The question we asked is pretty straight forward: 'If a full sensitive mapper finds a hit for a read, is a mapping tool able to locate a hit at the same position.' Regardless of the design of the tool, it should be ...
written 26 days ago by David Langenberger8.7k • updated 13 days ago by RamRS20k
3
votes
1
answer
666
views
1
answers
Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... We actually chopped the y-axis to visualise these minor differences, since people might be interested in exactly these. I think it is pretty clear that the y-axis is chopped and that the differences are minor. But thanks for highlighting it. We will add an extra note to the plot, to assure that the ...
written 26 days ago by David Langenberger8.7k
55
votes
1
answer
666
views
16 follow
1
answer
Forum: Best RNA-Seq aligner: A comparison of mapping tools
... RNA-Seq has replaced microarrays for many applications in the area of biomarker discovery. The prices have been fallen substantially in recent years. The sequence data allows to extract more information than gene expression only. And there is no requirement that a reference genome must exist. Howeve ...
genome forum ngs alignment rna-seq sequence written 26 days ago by David Langenberger8.7k

Latest awards to David Langenberger

Commentator 26 days ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Commentator 26 days ago, created a comment with at least 3 up-votes. For C: Repetitive Regions In Hg18
Appreciated 26 days ago, created a post with more than 5 votes. For A: Renaming Entries In A Fasta File
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Scholar 10 weeks ago, created an answer that has been accepted. For A: NGS pipeline analyses
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Renaming Entries In A Fasta File
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Repetitive Regions In Hg18
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Renaming Entries In A Fasta File
Appreciated 3 months ago, created a post with more than 5 votes. For A: Renaming Entries In A Fasta File
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bed File Of Reads To Wiggle File Of Numbers Of Features At Each Position
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Bed File Of Reads To Wiggle File Of Numbers Of Features At Each Position
Popular Question 5 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Renaming Entries In A Fasta File
Popular Question 6 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Popular Question 6 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Renaming Entries In A Fasta File
Librarian 6 months ago, created a post with more than 10 bookmarks. For Attention: Bowtie2 And Multiple Hits
Appreciated 7 months ago, created a post with more than 5 votes. For A: Renaming Entries In A Fasta File
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Renaming Entries In A Fasta File
Popular Question 9 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Popular Question 9 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Popular Question 10 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Popular Question 10 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology
Popular Question 11 months ago, created a question with more than 1,000 views. For Postdoc in bioinformatics – Department of Molecular Oncology

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1829 users visited in the last hour