User: simon.vanheeringen

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Posts by simon.vanheeringen

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Answer: A: How To Convert Bed Format To Gtf?
... And another alternative is to combine the UCSC tools `bedToGenePred` and `genePredToGtf`. bedToGenePred in.bed /dev/stdout | genePredToGtf file /dev/stdin out.gtf You can install these tools with bioconda, or download them [here][1]. [1]: http://hgdownload.cse.ucsc.edu/admin/exe/ ...
written 9 months ago by simon.vanheeringen160
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Answer: A: How can I see the distribution of TFBS on specific enhancer in UCSC
... You can check the ReMap UCSC track (based on ChIP-seq data): http://tagc.univ-mrs.fr/remap/index.php?page=browse And JASPAR 2018 has a UCSC track for predicted binding sites: http://jaspar.genereg.net/genome-tracks/ ...
written 10 months ago by simon.vanheeringen160
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Comment: C: Detecting expression in intergenic regions
... Would DERfinder be of use to you? > Here, we propose a novel method that first identifies differentially expressed regions (DERs) of interest by assessing differential expression at each base of the genome. The method then segments the genome into regions comprised of bases showing similar diffe ...
written 10 months ago by simon.vanheeringen160
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Answer: A: Which is a good source to download a reference genome?
... No matter what source you choose, try [genomepy][1] to download your genomes. Will include chromosome sizes, a BED file with gaps and, optionally, gene annotation. Works for Ensembl, UCSC and NCBI. Automated, scriptable and reproducable! ![genomepy example][2] [1]: https://github.com/simonvh/ge ...
written 10 months ago by simon.vanheeringen160
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Comment: C: BagFoot TF foot printing
... It does have support for ATAC-seq last I checked. Maybe not in the official release, might be in a branch in the github repo. ...
written 10 months ago by simon.vanheeringen160
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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 10 months ago by simon.vanheeringen160
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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 10 months ago by simon.vanheeringen160
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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 10 months ago by simon.vanheeringen160
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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 11 months ago by simon.vanheeringen160
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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 11 months ago by simon.vanheeringen160

Latest awards to simon.vanheeringen

Scholar 10 months ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?
Scholar 11 months ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?

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