User: Björn

gravatar for Björn
Björn650
Reputation:
650
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Trusted
Location:
Germany
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Last seen:
1 year ago
Joined:
5 years, 6 months ago
Email:
b**************@gmail.com

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Posts by Björn

<prev • 37 results • page 1 of 4 • next >
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Answer: A: How to obtain DrugBank Drug Name and SMILES Data from DrugBank ID?
... Mining the XML is one way, however probably the most complicated one. Instead you can download the drugbank SDF or SMILES file and map your IDs against these files to filter them for example. ...
written 12 months ago by Björn650
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Comment: C: pros- and cons- : programming skills vs. GUI
... You are never stuck in Galaxy. It's OpenSource and it's pretty easy to update tools or point the big community to update tools. Actually, for a few tools we have wrappers before the paper comes out, because more and more people talking to the Galaxy community and contributing to it during the publis ...
written 2.8 years ago by Björn650
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Answer: A: pros- and cons- : programming skills vs. GUI
... For our teaching courses, and from your question I think we are targeting the same audience, we try to take the fear from our students. For this we train them in Galaxy and demonstrate how easy reproducible science and HPC computing can be. If you can make the point that everyone can reproduce (or n ...
written 2.8 years ago by Björn650
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Answer: A: Galaxy Based GATK Realigner Target Creator
... Hi, Galaxy related questions are usually better to ask here: http://biostar.usegalaxy.org/ Nevertheless, this does not seem like a Galaxy problem. It seems you have used different reference genomes. One set of genome (annotations) is based on the chromosome naming scheme (1,2,3,4) and the other is ...
written 3.5 years ago by Björn650
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Comment: C: deepTools: user-friendly tools for the normalization and visualization of deep-s
... Hi, the binSize parameter depends on several factors, like depth of sequencing or scaffold of enriched peeks (sharp or broad). Imho if you have broader regions or less sequencing depth you should use a higher binSize (10kb). Smaller values can be used by sharp regions or a high coverage. Hope this ...
written 3.9 years ago by Björn650
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Comment: C: deepTools: user-friendly tools for the normalization and visualization of deep-s
... Hi, such an enhancement would be relatively easy to implement in deepTools. I have created a github issue under https://github.com/fidelram/deepTools/issues/56 and we will try to implement it. PR are always welcome :) Thanks for that suggestion! Bjoern ...
written 4.3 years ago by Björn650
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Answer: A: What is the best programming language for NGS data analysis pipeline development
... If reproducibility, transparency and accessibility are key factors of your pipeline I would recommend the Galaxy API for pipeline development. Maybe that sounds strange, but Galaxy provides many different abstractions layers that will save you hours of work. For example do you care about tool versi ...
written 4.3 years ago by Björn650
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Tool: deepTools: user-friendly tools for the normalization and visualization of deep-sequencing data
... deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepT ...
chip-seq visualisation qc tool rna-seq written 4.3 years ago by Björn650 • updated 3.9 years ago by xfliwz50
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Comment: C: ngs.plot: Quick mining and visualization of next-generation sequencing data by i
... Propably deepTools: https://github.com/fidelram/deepTools/wiki You can also find it in the Galaxy Tool Shed. Cheers, Bjoern ...
written 4.3 years ago by Björn650
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Answer: A: Comparing And Plotting Coverage Between Two Bam Files
... Hi, the recently published deepTools should do what you are searching for. You can normalize your BAM files and compare them as you like in the end you can generate some nice plots. For more information have a look at the deepTools wiki. As a bonus, deepTools is available in the Galaxy Tool Shed ...
written 4.4 years ago by Björn650

Latest awards to Björn

Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Heatmap Of Read Coverage Around Tsss
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Is Galaxy Ok For Speed?
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Is Galaxy Ok For Speed?
Scholar 4.3 years ago, created an answer that has been accepted. For A: Heatmap Of Read Coverage Around Tsss
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Heatmap Of Read Coverage Around Tsss
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: Heatmap Of Read Coverage Around Tsss
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Heatmap Of Read Coverage Around Tsss
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Is Galaxy Ok For Speed?

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