User: simon.vanheeringen

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Posts by simon.vanheeringen

<prev • 26 results • page 2 of 3 • next >
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Answer: A: Motif prediction in Chip-seq data
... All of them! :) This is why I wrote [GimmeMotifs][1]. It uses an ensemble of motif prediction tools and chooses the best non-redundant motif from the results. From benchmarking on ENCODE ChIP-seq data, Homer, MEME and BioProspector show the overall best performance. However, there is no single tool ...
written 2.8 years ago by simon.vanheeringen200
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Answer: A: GC & AT content calculation
... You can use bedtools. bedtools nuc -fi /data/genomes/hg38/hg38.fa -bed input.bed | cut -f1-5 #1_usercol 2_usercol 3_usercol 4_pct_at 5_pct_gc chr1 28216 31238 0.465255 0.534745 chr1 51379 52104 0.478621 0.521379 chr1 136251 145899 0.473984 0.526016 ...
written 2.8 years ago by simon.vanheeringen200
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Answer: A: BagFoot TF foot printing
... Not sure how well it compares, but I found http://pythonhosted.org/pyDNase/ to be very straightforward to run. ...
written 2.8 years ago by simon.vanheeringen200
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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 2.8 years ago by simon.vanheeringen200
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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 2.8 years ago by simon.vanheeringen200
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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 2.8 years ago by simon.vanheeringen200
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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 2.9 years ago by simon.vanheeringen200
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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 2.9 years ago by simon.vanheeringen200
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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 2.9 years ago by simon.vanheeringen200
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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 2.9 years ago by simon.vanheeringen200

Latest awards to simon.vanheeringen

Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Identifying the orientation of a CTCF motif?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?

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