Moderator: David Langenberger
David Langenberger ♦ 8.7k
- 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
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... 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 Langenberger ♦ 8.7k
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... STAR looks similar and Tophat2 not so good. Now I'm curious about Tophat2, too. :) ...
written 26 days ago by
David Langenberger ♦ 8.7k
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... 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 Langenberger ♦ 8.7k
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... 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 Langenberger ♦ 8.7k
• updated
13 days ago by
RamRS ♦ 20k
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... 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 Langenberger ♦ 8.7k
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... 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 Langenberger ♦ 8.7k
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... 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 Langenberger ♦ 8.7k
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... 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 Langenberger ♦ 8.7k
• updated
13 days ago by
RamRS ♦ 20k
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... 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 Langenberger ♦ 8.7k
55
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16 follow
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... 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 ...
written 26 days ago by
David Langenberger ♦ 8.7k
Latest awards to David Langenberger
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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: Converting Sam Files To Bam Files - Reproduce Results Nature Paper: Transcriptom
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26 days ago,
created a comment with at least 3 up-votes.
For C: Repetitive Regions In Hg18
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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
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11 weeks ago,
created a post with more than 5 votes.
For A: Renaming Entries In A Fasta File
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12 weeks ago,
created a comment with at least 3 up-votes.
For C: Repetitive Regions In Hg18
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3 months ago,
created an answer that was upvoted at least 5 times.
For A: Renaming Entries In A Fasta File
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For A: Renaming Entries In A Fasta File
Teacher
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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
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5 months ago,
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For Postdoc in bioinformatics – Department of Molecular Oncology
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created an answer that was upvoted at least 5 times.
For A: Renaming Entries In A Fasta File
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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,
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For A: Renaming Entries In A Fasta File
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6 months ago,
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For Attention: Bowtie2 And Multiple Hits
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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
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