User: Fidel

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Fidel1.9k
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Germany
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Researcher at the Max Planck Institute for Immunobiology and Epigenetics.

Posts by Fidel

<prev • 157 results • page 1 of 16 • next >
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Comment: C: TAD calling with HiCExplorer - TypeError in hicFindTADs TAD_score
... thanks for the report. We will look into that. ...
written 18 months ago by Fidel1.9k
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Comment: C: TAD calling with HiCExplorer - TypeError in hicFindTADs TAD_score
... This is strange. Can you tell us which version of HiCExplorer are you using. Can you run `hicMergeBins`to reduce the size of the matrix and try to plot it using `hicPlotMatrix`. This is to check that the chromosomes are properly encoded in HiCExplorer matrix object. ...
written 18 months ago by Fidel1.9k
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Comment: C: How To Use Bwa To Find Restriction Enzyme Coordinates In A Genome
... I just updated the github page to use the reverse_complement. I tested the new code with one instance of a non-palindromic enzyme and compared the results with Emboss remap. Thanks for pointing out the error. ...
written 2.2 years ago by Fidel1.9k
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Comment: C: How To Use Bwa To Find Restriction Enzyme Coordinates In A Genome
... You are right! Should be the `reverse_complement()` function. Because all restriction enzymes that I know are palindromic I always get the correct answer in my tests. This is so embarrassing :( ...
written 2.2 years ago by Fidel1.9k
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Comment: C: How To Use Bwa To Find Restriction Enzyme Coordinates In A Genome
... That line returns the reverse complement of the motif (referred as `pattern`) pattern = "ACGT" str(Seq(pattern, generic_dna).complement()) 'TGCA' Then, the motif and reverse complement of the motif are searched on the DNA sequence on the fasta file. Finally, the resulting bed file is ...
written 2.2 years ago by Fidel1.9k
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Comment: C: How To Use Bwa To Find Restriction Enzyme Coordinates In A Genome
... I hope there is no bug. I tested the results and so far the only problem I found was with upper/lower case DNA strings that I initially overlooked. What would be your concern with the reverse complement? ...
written 2.2 years ago by Fidel1.9k
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Comment: C: How To Use Bwa To Find Restriction Enzyme Coordinates In A Genome
... At the time I needed something that I could add to our set of tools to process and analyze Hi-C data. Having Emboss or GBrowse2 as dependencies just to find restriction sites was not worth (BWA was already a dependency). The solution using bio-python is so simple that I didn't mind re-implementing ...
written 2.2 years ago by Fidel1.9k
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Answer: A: Do specialized Hi-C databases exist?
... We have been working on an initiative to host and visualize Hi-C data. We download the data from SRA and processes it with our pipeline to generate downloadable matrix files (stored on hdf5 files). So far we have some data for drosophila, mouse and human available. The website is: http://chorogen ...
written 2.2 years ago by Fidel1.9k
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Answer: A: TUTORIALS about Hi-C data analysis
... You can use [HiCExplorer][1], here is a tutorial: http://hicexplorer.readthedocs.io/en/latest/content/example_usage.html [1]: http://hicexplorer.readthedocs.io/ ...
written 2.2 years ago by Fidel1.9k
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Answer: A: How To Use Bwa To Find Restriction Enzyme Coordinates In A Genome
... Here is an update for people landing on this question: The bwa method that I proposed does not work properly. I don't remember exactly why it was wrong but I stop using it. I think it was returning regions with NNNs. My solution was to use Biopython to search for a pattern. This is quite fast and a ...
written 2.2 years ago by Fidel1.9k

Latest awards to Fidel

Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: what is the meaning of "degenerative nature" of Chip-seq
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: what is the meaning of "degenerative nature" of Chip-seq
Appreciated 24 months ago, created a post with more than 5 votes. For A: Visualization Of Read Count On Genome
Scholar 24 months ago, created an answer that has been accepted. For A: Different qualities of genomes - Is there a standard/definition?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: what is the meaning of "degenerative nature" of Chip-seq
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Visualization Of Read Count On Genome
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Visualization Of Read Count On Genome
Autobiographer 2.2 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Different qualities of genomes - Is there a standard/definition?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How To Use Bwa To Find Restriction Enzyme Coordinates In A Genome
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Visualization Of Read Count On Genome
Great Question 2.4 years ago, created a question with more than 5,000 views. For Is There Any Advantage Of Paired End Sequencing For Chip-Seq?
Great Question 2.8 years ago, created a question with more than 5,000 views. For Is There Any Advantage Of Paired End Sequencing For Chip-Seq?
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Different qualities of genomes - Is there a standard/definition?
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Visualization Of Read Count On Genome
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: what is the meaning of "degenerative nature" of Chip-seq
Scholar 2.8 years ago, created an answer that has been accepted. For A: Different qualities of genomes - Is there a standard/definition?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Visualization Of Read Count On Genome
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Visualization Of Read Count On Genome
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Visualization of ChIP-seq data using Heatmaps (Updated: 03/10/16)
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Visualization Of Read Count On Genome
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Visualization of ChIP-seq data using Heatmaps (Updated: 03/10/16)
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Visualization Of Read Count On Genome
Scholar 3.1 years ago, created an answer that has been accepted. For A: Different qualities of genomes - Is there a standard/definition?
Scholar 3.3 years ago, created an answer that has been accepted. For A: Different qualities of genomes - Is there a standard/definition?

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