More posts like this
-
identify unmapped regions
written by María José 1Hi, We've created a coverage file of the aligments against the GRCh38 reference genome and we are currently trying to identify regions with zero coverage. …
-
Define enhancer regions
written by Faiza 1Hi! I need to get enhancer regions from publicly available data e.g ENCODE. Encode contain Histone marks bigwig file which is Signal p value and …
-
Annotation of ATAC-seq peak - distal intergenic regions as enhancers
written by Pei 26Hi! I just read a [paper][1] and in Fig. 1, the authors provided a "typical peak annotation pie chart shows that more than half of …
-
Identify binding motifs within large super enhancer region
written by mkunika 0Hello, From my H3K27ac ChIP seq data, I have identified 500 super enhancer regions using Homer's findPeaks -style super. From the super enhancer regions, I …
-
DESeq2 for comparison of enhancer activity (eRNA)
written by marionette.kent 0Hi community, My colleague recently tries to compare enhancer activity of control and knockdown cell line using total RNA-Seq. Total RNA-Seq data was used to …
-
how can i quantify expression using own my gff ?
written by dlyedms1019 0Hi, I want to quantify the leads in my defined region. This is not a gene, but an enhancer region. (from ENCODE) The data is …
-
database for searching introns or exons which contain known binding site
written by qwesxadzc9 0Dear all， is there any database can search for genes which contain known exonic or intronic splicing enhancer? For instance, I want to get some …
-
Comprehensive annotations for rat
written by bioinfc37 3Seeking the most comprehensive database for the rat models (rn5) or a pipeline to generate a richer annotation for this organism.
-
All possible predicted RNA in mm9 genome
written by bioinfc37 3Seeking a database of all possible predicted RNA in the entire mm9 genome. mfold will do this but has a 9000 base limit. I'm sure …
-
Annotating SNPs for promoter and enhancer regions
written by siddharth.sethi5 30Hi Everyone, I am trying to annotate Snps and identify those snps which fall within promoter and enhancer regions. I am doing this using Mouse …
If you have access to raw / or RPKM normalized bedGraph files for DNase, H3K4me1, H3K4me3, and H3K27Ac then you can use my tool CIPHER to predict potential enhancer elements. If you don't have access to these ChIP-seq/DNase-seq datasets and you can't find them for your preferred cell line in ENCODE / Roadmap Epigenetics then you're best bet is to look into a database like EnhancerAtlas.
Goodluck!
Hello bioinfc37!
We believe that this post does not fit the main topic of this site.
Unspecific. OP never followed up.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!