User: simon.vanheeringen

Reputation:
150
Status:
Trusted
Location:
Last seen:
3 months ago
Joined:
10 months ago
Email:
s*****************@gmail.com

Posts by simon.vanheeringen

<prev • 21 results • page 1 of 3 • next >
0
votes
4
answers
10k
views
4
answers
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 6 months ago by simon.vanheeringen150
1
vote
2
answers
442
views
2
answers
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 7 months ago by simon.vanheeringen150
0
votes
1
answer
479
views
1
answers
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 7 months ago by simon.vanheeringen150
1
vote
3
answers
357
views
3
answers
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 7 months ago by simon.vanheeringen150
1
vote
3
answers
680
views
3
answers
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 7 months ago by simon.vanheeringen150
0
votes
1
answer
426
views
1
answers
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 7 months ago by simon.vanheeringen150
2
votes
1
answer
379
views
1
answers
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 7 months ago by simon.vanheeringen150
1
vote
3
answers
680
views
3
answers
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 7 months ago by simon.vanheeringen150
4
votes
1
answer
668
views
1
answers
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 8 months ago by simon.vanheeringen150
0
votes
2
answers
490
views
2
answers
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 months ago by simon.vanheeringen150

Latest awards to simon.vanheeringen

Scholar 7 months ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?
Scholar 8 months ago, created an answer that has been accepted. For A: Identifying the orientation of a CTCF motif?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1380 users visited in the last hour