GetPeakTags - finds sequencing tags associated with genomic positions. ![]() HomerTools freq - finds nucleotide/dinucleotide frequencies of a collection of sequence and GC/CpG content. HomerTools extract - extract genomic sequence for peaks from a peak file. (see SIMA analysis)Īdditional Utilities that may be useful (and sub-programs used by those above)Ī,, - tools for joining/merging tab separated flat files Novel tool to boost sensitivity by pooling features together when performing interaction calculations. calculates the difference in correlation profiles between two Hi-C experiments (see Hi-C PCA analysis)į - find continuous or differential regions from PCA/corrDiff results that describe what compartment regions of DNA belong to (see Hi-C PCA analysis)įindHiCInteractionsB圜hr.pl - helps automate the finding of high-resolution intra-chromosomal interactions (see Finding Hi-C Interactions)Ī - program for re-analysis of significant interactions, such as relating them to ChIP-Seq peaks (see Annotating Interactions) automated PCA analysis on Hi-C data to identify "compartments" (see Hi-C PCA analysis) creates a new motif file from a consensus sequenceĪnalyzeHiC - primary analysis program - generates interaction matrices, normalization, identification of significant interactions, clustering of domains, generates Circos plots (most of the following programs use this one internally, See Hi-C analysis) creates a new motif file reflecting the nucleotide preferences of the opposite strand. creates a PNG or PDF logo from any motif file. remove reads found outside acceptable chromosome limitsĪ - annotation of de novo identified transcriptsĬ - checks a library of motifs for known motifs, creates in HTML output summarizing motif results (described here). output tag directory as an alignment BED file (See Miscellaneous)ī, - convert between HOMER peak file format and BED file format (See Miscellaneous)Ĭ - use this to see if your peak file is in the correct format HomerTools - basic sequence manipulation (See Sequence Manipulation) MergePeaks - find overlapping peak positions (See Comparing ChIP-Seq Peaks) (See Annotating Peaks, Quantification)Ī - quantification of RNA levels across transcripts (See RNA quantification)Ī - quantification of RNA levels across repeats (documentation coming soon.) MakeUCSCfile & - create bedGraph file for visualization with the UCSC Genome Browser (See Creating UCSC file)įindPeaks - find peaks in ChIP-Seq data, regions in histone data, de novo transcripts from GRO-Seq (See Finding ChIP-Seq Peaks)Ī - automation of programs found above (See Automation of ChIP-Seq analysis)Ī - annotation of genomic positions, organization of motif and sequencing data, histograms, heatmaps, and more. MakeTagDirectory - creates a "tag directory" from high-throughput sequencing alignment files, performs quality control (See Creating a Tag Directory) ![]() Next-Gen Sequencing/Genomic Position Analysisį - performs motif analysis from genomic positions (See Finding Motifs from Peaks) setup custom promoter sets for specialized analysis (See Customization) Homer2 - core component of motif finding (Called by everything else, See FASTA file analysis)į - performs motif and gene ontology analysis with lists of Gene Identifiers, both promoter and mRNA motifs (See Gene ID Analysis Tutorial)į - performs only gene ontology analysis with lists of Gene Identifiers (Called by, See Gene Ontology Analysis) Running each program without any arguments will provide basic instructions and a list of command line options.į - performs motif analysis with lists of Gene Identifiers or FASTA files (See FASTA file analysis) Below is a quick introduction to the different programs included in HOMER.
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