User: simon.vanheeringen

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Posts by simon.vanheeringen

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Answer: A: Identifying the orientation of a CTCF motif?
... Use the CTCF motif to scan the peaks. The directionality of the motif match presumably tells you the CTCF orientation. For instance, you can use this CTCF motif (save in a tab-separated text file): >C2H2_ZF_Average_200 0.081779124449 0.816566257007 0.0503624700168 0.0512921485275 ...
written 2 days ago by simon.vanheeringen50
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Answer: A: motif in set of genes
... You can use [GimmeMotifs][1] (disclaimer: I am the author). You will have to use a motif representation (positional frequency matrix) that looks like this: >motif_name 0 0 0 1 0.2 0 0 0.8 Then you can use `gimme scan` to scan with this motif: $ gimme scan seq ...
written 8 days ago by simon.vanheeringen50
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Answer: A: picard installation failure
... Try using [bioconda][1]. After installation of Anaconda and setting up the bioconda repository, you can install Picard tools like this: $ conda install picard [1]: https://bioconda.github.io/ ...
written 8 days ago by simon.vanheeringen50
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Answer: A: Does anyone know where to get individual feline chromosome fasta file?
... Use [genomepy][1] to make your life easier: $ genomepy install felCat8 UCSC [1]: https://github.com/simonvh/genomepy ...
written 17 days ago by simon.vanheeringen50
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Answer: A: Visualization for ChIP-seq analysis
... For TF motif analysis you can use [GimmeMotifs][1]. It uses an ensemble of different programs (including Homer, MEME and BioProspector which are, in my experience, the top performing programs) for *de novo* motif discovery. [Fluff][2] contains some nice options for ChIP-seq visualization. Disclai ...
written 20 days ago by simon.vanheeringen50
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Answer: A: ATACseq with STAR and macs2
... Have you tried the pipeline from the Kundaje lab? https://github.com/kundajelab/atac_dnase_pipelines Pretty much worked out of the box for me. For differential peaks you could do the following: 1. merge all peaks into one peak set 2. count reads for all experiments in this merged peak set (usi ...
written 29 days ago by simon.vanheeringen50
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Answer: A: Feature/Motif Extraction from Sequences?
... Given your clarification, I think kmer-SVM does exactly what you want. You can train and evaluate performance (using cross-validation). The SVM model can then be used to predict new sequence. The k-mers will have associated weights, that you would be able to cluster, match to known motifs, etc. ...
written 29 days ago by simon.vanheeringen50
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Comment: C: Feature/Motif Extraction from Sequences?
... I would say it wholly depends on the nature of your subsequent downstream comparison. What is the question and with what purpose do you want to do the analysis? Can you clarify? There's a whole body of work on k-mer/motif analysis, and you might not want/need to re-invent the wheel. For instance, i ...
written 4 weeks ago by simon.vanheeringen50
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Answer: A: Genome Browser suggestions
... Why not use the [UCSC Genome Browser][1]? You can add tracks using track hubs and support non-standard genomes using assembly hubs, see here: https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html. The advantage of track hubs is that you only have to create them once, and then you can use alway ...
written 7 weeks ago by simon.vanheeringen50
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Tool: GimmeMotifs 0.11.1: for all your transcription factor motif needs
... I'm happy to announce the latest release of **GimmeMotifs** (0.11.1) GimmeMotifs is an analysis framework for transcription factor motif analysis written in Python. It contains command-line scripts to predict de novo motifs, scan for known motifs, identify differential motifs, calculate motif enric ...

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Scholar 2 days ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?

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