Tag: HOMER

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

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Genome hg19**not found in homer config

I want to use the Homer to do annotation. After I input “annotatePeaks.pl 31512_TH0_D0.bed hg19 > 31512_TH0_D0.ann.txt” , it shows “!!!!Genome hg19 not found in /home/jenny/NGStools/homer/.//config.txt” I used the command “perl /home/jenny/NGStools/homer/configureHomer.pl -install hg19” to install it, and I am sure I installed the hg19 for the homer Then input…

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Convert bedGraph to Homer tag directory?

Convert bedGraph to Homer tag directory? 0 Hi, I am new to ChIP-seq analysis. When taking published data in .bedGraph format (generated by Homer), is there any way to convert back to Homer tag directory? (other than aligning from the raw .fasta). I suppose extracting columns into .bed format and…

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Create junctions from Bed file for IGV visualization

Create junctions from Bed file for IGV visualization 0 Any advice for creating junctions file from a bed-like file? My bed file looks like this: chr start end chr star end I have tried to copy the format used in TopHat (junctions file). But I can’t see the junctions in…

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How to map query coordinates on to genome gff annoation files ?

How to map query coordinates on to genome gff annoation files ? 0 Hello Researchers I have a project where i got stuck on :- mapping query coordinates on to gff annoation files, means i have to find all the total counts of gene, mRNA, exon, CDS, 3′-utr, 5′-utr, promoter,…

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merging .narrowPeak files with all of the columns they have

merging .narrowPeak files with all of the columns they have 0 Hello, I want to ask about merging concept of .narrowPeak files generated by macs2. I am merging them with HOMER mergePeaks as I found the most informative one (compared to the bedops, bedtools). However, for the downstream analyses I…

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How to prepare HiCUP output as input for HOMER?

HiC analysis: How to prepare HiCUP output as input for HOMER? 0 Hi everyone, I am new to HiC and using HiCUP to analyse HiC data (I will try other pipelines and combination of software eventually). /tools/hicup –zip –bowtie2 /tools/bowtie2-2.3.4.1-linux-x86_64/bowtie2 –index /hg38/hg38 –digest /hg38/Digest_hg38_HindIII_None_15-12-15_27-10-2021.txt R1.fastq R2.fastq For now, I aligned…

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Frontiers | Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses

Introduction Phytoplasmas are wall-less bacterial pathogens that are known to infect numerous plant species and lead to significant agricultural losses (Gurr et al., 2016; Kumari et al., 2019; Pierro et al., 2019). They are parasitic bacteria multiplying exclusively in phloem sieve elements and are transmitted between plants by phloem-feeding insects…

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Exavir Therapeutics announces preclinical data demonstrating complete elimination of HIV from human cells with LNP-delivered Tat-targeted CRISPR-Cas9

Early candidate from XVIR-TAT series demonstrated genetic elimination of HIV and robust anti-retroviral activity with CRISPR-Cas9 based excision Exavir lipid nanoparticles (LNPs) with mRNA encoding Cas9 nuclease and proprietary Tat-targeted gRNAs demonstrated up to 100% HIV suppression in infected human cells Exavir is optimizing LNP formulations for tissue tropism, and…

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ChIP-seq analysis differential peak analysis regarding spike-in

ChIP-seq analysis differential peak analysis regarding spike-in 0 Hi, I have 4 human ChIP-seq datasets, including drug A treated H3K4me3 and IgG, and drug B treated H3K4me3 and IgG. Meanwhile, sacCer3 spike-in data is added to human ChIP-seq data. Here is what I did: After aligning, I got 8 bam…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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Finding Instance of Specific Motifs

Homer – Finding Instance of Specific Motifs 0 Hello everyone! I’m relatively new to bioinformatics, so sorry if this question sounds silly! I have started to use Homer to find a specific motif in a list of genes. The matter is: when I run findMotifsGenome.pl using -find <motif file> ,…

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Zero peaks detected using findMotifsGenome.pl

Hi, I am extremely new to this, so apologies in advance for any mistakes in my post! I am trying to use findMotifsGenome.pl in Homer to identify transcription factor motifs based on genomic coordinates, but I always get a message that no peaks are detected. I’ve tried various different input…

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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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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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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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