User: Mads Lerdrup

gravatar for Mads Lerdrup
Mads Lerdrup440
Reputation:
440
Status:
Trusted
Location:
Denmark / Copenhagen / BRIC
Website:
http://easeq.net/
Twitter:
MadsLerdrup
Last seen:
2 years ago
Joined:
2 years, 11 months ago
Email:
m***********@bric.ku.dk

Old school biologist. After realizing that I did not do well in rubber boots, I spent a lot of time in the lab and by the confocal doing live cell imaging, but I always lived for the subsequent data analysis.

When I graduated data were sparse and each data point required an effort. With the data-abundance now, the challenge is to focus on the relevant questions and make the investigation and comprehension of the data as intuitive and effortless as possible.

Since I joined BRIC, I have been analyzing the group’s ChIP-seq (and other seq data). I have always been puzzled why seq data requires biologists to write and understand scripting, when other complex data such as high dimensional microscopy, flow cytometry, and high content screening do not.

I kept waiting for someone to make a more intuitive, interactive and visual solution for this, and eventually made my own. The result is called EaSeq and was published recently – you can take a look here: http://easeq.net/ , here: http://dx.doi.org/10.1038/nsmb.3180 and here: https://youtu.be/4_DhQ24qWlk

I’d of course claim that EaSeq will enable a larger group of people to investigate and make use of ChIP-seq data, and even that seasoned people can speed up some processes too, but I trust your judgement more than mine on this :-)

Posts by Mads Lerdrup

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Which ChIP-seq IgG to use?
... I think that it is arguable wether input represents the actual background in a ChIP-seq better than an IgG control, but probably a lot of considerations went into this, so I'll gladly stand corrected :-) As I see it, then the background might be affected by carry-over as you mention, and more or le ...
written 2.4 years ago by Mads Lerdrup440
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... A short update. It is not off the table, but so far the porting is unsuccessful and will require more time that I initially hoped for. I have discovered that cloud-based Virtual Desktops are becoming very common and affordable. So essentially you don’t need to install Windows, but can run it from t ...
written 2.4 years ago by Mads Lerdrup440
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... I just had the same question posted on the chat-forum within EaSeq (it might have been you?), so I’ll just summarize my replies for other forum users: Virtually all plot types, including heatmaps, will need to wait for Regionsets and Datasets that are used for the visualization to be released from ...
written 2.4 years ago by Mads Lerdrup440
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... Two notes: I am out of Office, so I wont be able to look at it before wednesday. Visualization of coverage files (bedgraph and wig) is slower than read files (e.g. bed and bam). ...
written 2.5 years ago by Mads Lerdrup440
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... Odd. Can you please send me a link to one of the files that gives you troubles. Then I’ll debug the import. If you don't already do it, then I would recommend that you save a session containing your imported data after import. That will save you quite some time. Importing the reads from bed files ...
written 2.5 years ago by Mads Lerdrup440
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... Did I understand your question correctly? The peaks are stored as a bed file, and you try to import this file and nothing else. In that case the peaks should be imported as a regionset. They are no longer considered as the chipseq data, but as a derived set of regions. To make figures you will als ...
written 2.5 years ago by Mads Lerdrup440
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Comment: C: ChIP-Seq: When reducing paired end reads to one coordinate, should I use the mid
... That is always the question - how much flexibility should you add on the cost of reducing user-friendlyness. What is your target group? What level of experience do you expect them to have? And how often do you believe they will run the software? And also, how central is that part of the workflow for ...
written 2.5 years ago by Mads Lerdrup440
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Answer: A: ChIP-Seq: When reducing paired end reads to one coordinate, should I use the mid
... What a well-timed and IMHO interesting post :-) I am working on adding paired end (PE) support to [EaSeq][1], and I am going through exactly the same considerations and do not have any prior experience with PE as we have not used it for ChIP at our institute (yet). EaSeq also works with a single in ...
written 2.5 years ago by Mads Lerdrup440
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Comment: C: Visualization of ChIP-seq data (mapped reads)
... I know that I use a different approach, but I tried to map with bowtie and import the FoxP3 ChIP-seq into [EaSeq][1] (default settings) to see how it looked like. And I think that the peak-containing structure is remade better than in the example that you posted above (see image). IMHO then the bins ...
written 2.6 years ago by Mads Lerdrup440
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... So do I. Rest assured that I'll shout out it loud, if I make a succesful porting to mac and linux :-) ...
written 2.7 years ago by Mads Lerdrup440

Latest awards to Mads Lerdrup

Popular Question 2.2 years ago, created a question with more than 1,000 views. For EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
Scholar 2.5 years ago, created an answer that has been accepted. For A: Motif not found for protein used for IP?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How quantitative is Chip-seq?
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: How quantitative is Chip-seq?
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: How quantitative is Chip-seq?
Supporter 2.8 years ago, voted at least 25 times.
Appreciated 2.8 years ago, created a post with more than 5 votes. For EaSeq - Interactive ChIP-seq analysis and visualization
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How quantitative is Chip-seq?
Autobiographer 2.8 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.8 years ago, created an answer that has been accepted. For A: Motif not found for protein used for IP?
Appreciated 2.9 years ago, created a post with more than 5 votes. For EaSeq - Interactive ChIP-seq analysis and visualization

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