Category: HOMER

Workshop proceedings: GWAS summary statistics standards and sharing: Cell Genomics

Introduction Genome-wide association studies (GWASs) have brought enormous progress in mapping the genetic basis of common diseases or traits, 1 Visscher P.M. Wray N.R. Zhang Q. Sklar P. McCarthy M.I. Brown M.A. Yang J. 10 years of GWAS discovery: Biology, function, and translation. , 2 Claussnitzer M. Cho J.H. Collins…

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The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial

Alfaro-Nunez A, Bertelsen MF, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Olsen MT et al. (2014) Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 14:206 PubMed  PubMed Central  Article  Google Scholar  Ali OA, O’Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C et al….

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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Homer finds same peak multiple times

I am using Homer to identify peaks in RNA-seq data and then determine differential expression by counting reads per peak. Homer has a lovely package that does just this: getDifferentialPeaksReplicates.pl. The issue is that for some reason Homer returns the same peak multiple times in its final output (Bonus question:…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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Oakland Zoo Invites Public to Relinquish Personal Effects Made From Exotic Animals To Help End the Illegal Wildlife Trade – Oakland News Now

Tag CloudSam Cassidy, Rally at Lake Merritt, Soulbeat Day, Kofi Bonner on future of office work after Pandemic, The Battery SF Club, Oakland Redevelopment Agency, Community Revitalization and Investment Authority , California Capital Investment Group, IFTTT Pro, Bellevue Club Lake Merritt, Michael Birch, Xochi Birch, website, OaklandNewsNow.com, French Open Tennis,…

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How to get the genes from an identified motif using HOMER?

How to get the genes from an identified motif using HOMER? 0 On my RNA-seq data, I ran the HOMER script: findMotifs.pl /Users/A/Desktop/AA.txt human RNA_sample/ -start -500 -end 500 -len 8,10 -p 4 And I got: Now, my question is, how can I get ALL the genes included in the…

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Interpreting TFBS enrichment from random genomic regions

Hi all, To make a long story short, my lab has developed a computational method for analyzing WGBS data that results in genomic regions of interest. These are regions defined by sequencing reads with mixed methylation states (i.e. consecutive CpGs having non-matching methylation). My boss wants me to use some…

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Can I adding (multiply ) the P-value of one Transcriptioin factor identified by two motif?

Can I adding (multiply ) the P-value of one Transcriptioin factor identified by two motif? 0 Hi, I am using Homer to identify motif in a set of genomic regions, then I get a list of motifs with a list of best-matched transcription factors(TF). most of the time I get…

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Can I use the summits.bed from MACS2 on HOMER

Can I use the summits.bed from MACS2 on HOMER 1 I understand that to run HOMER you need BED files, so could I use the BED output file from “macs2 callpeak” to run “findMotifsGenome.pl”? Homer Macs callpeak bed • 40 views • link updated 2 hours ago by seidel 8.3k…

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Problem with HOMER -find

Problem with HOMER -find <motif file> 0 I am trying to search for specific motifs in my set of promoters. It should be possible with the option -find *.motif I know that there are for sure some occurrences because I have found them with search function in Notepad. However HOMER…

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HOMER hg19 not found in config.txt

Hi! I am trying to run findMotif.pl from HOMER, in order to detect some regulatory motifs in a set of fasta sequences. When I type: findMotifs.pl sequences.fasta hg19 . I get the following error: !!! hg19 not found in /mnt/lustre/scratch/home/programs/HOMER/.//config.txt Try typing “perl /mnt/lustre/scratch/home/programs/HOMER//.//configureHomer.pl -list” to see available promoter sets…

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Comment: Direct – indirect binding of a transcription factor in chip-seq analysis

Try with different tools HOMER, MEME etc. May be try +/- 10bp from summit of peak. If same motif comes out than the probability increase for direct binding. Although this approach is just to get an idea that there is a direct interaction. Source link

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