User: simon.vanheeringen

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Posts by simon.vanheeringen

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Best tool for Motif enrichment of TFs
... Yes. The subtool `gimme roc` from GimmeMotifs can do this (as can Homer and many other tools). For GimmeMotifs, you can install it via bioconda and run the following command: $ gimme roc subset.fa all_promoter.fa -r roc.report Here `subset.fa` are your promoters of interest and `all_promoters. ...
written 19 days ago by simon.vanheeringen170
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Answer: A: Best tool for Motif enrichment of TFs
... Try [GimmeMotifs][1]! You can scan for known motifs, or identify *de novo* motifs. Amongst many other tools, both MEME and homer are included as *de novo* motif finding tools. [1]: http://gimmemotifs.readthedocs.io ...
written 5 weeks ago by simon.vanheeringen170
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Answer: A: Consensus motif of closely related TFs
... You can cluster the PWMs. One option is to use [GimmeMotifs][1] (disclaimer: I wrote the software). The command `gimme cluster` can be used. There are also other tools that can do this, such as RSAT. [1]: https://gimmemotifs.readthedocs.io ...
written 8 weeks ago by simon.vanheeringen170
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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 12 months ago by simon.vanheeringen170
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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 13 months ago by simon.vanheeringen170
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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 13 months ago by simon.vanheeringen170
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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 13 months ago by simon.vanheeringen170
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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 13 months ago by simon.vanheeringen170
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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 13 months ago by simon.vanheeringen170
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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 13 months ago by simon.vanheeringen170

Latest awards to simon.vanheeringen

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Identifying the orientation of a CTCF motif?
Scholar 13 months ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?
Scholar 13 months ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?

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