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• Motif Search from Bed file
  Hi all, I have recently generated a list of motifs of TF binding sites within peaks of my ChIPse...
• Homer for Motif search
  Hi,    I would like to use HOMER to search for enriched motif on a ChIPseq analysis I did using ...
• Motif discovery-Chip seq
  Hello, I am analyzing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads wi...
• Input: gene name (UCSC-style) Desired output: promoter sequences in FASTA format
  Hi everyone! I have a list of 450 gene names for which I need to find the promoter sequences (I ...
• The Last Column In The Output File Of 'Screen Motif'
  Hi, I was using the tool 'Screen Motif' to find a particular motif in given region of genome. ...
• Get fasta file from peak called BED file to do Motif analysis
  Hi all, I have some called peaks in BED format and would like to extract the sequences in a FAST...
• Isolating core sequences ("summits") of BED or FASTA files
  This seems like it should be self-explanatory, but I can't figure it out - apologies in advance. ...
• Search For Tf Binding Site Patterns In Galaxy
  I am trying to come up with a nice workflow/tutorial for the use of Galaxy to search for Transcr...
• HOMER motif search, conservation and correlate ChIP-seq to RNA-seq
  Hi there, I need help or advice in the following questions which may not be related to each othe...
• Problem With Gatk Tools Not Accepting Bam File As Input
  I am using GATK tools on the useGalaxy main server to detect variants in a mutant C. elegans whol...
• De-Novo Motif Analysis
  Two questions - 1. When I call peaks with MACS on Galaxy I get different results than if I run MA...
• De-Novo Motif Analysis
  Two questions - 1. When I call peaks with MACS on Galaxy I get different results than if I run MA...
• filter by fasta ids
  Hi. I am new to using Galaxy and I'm trying to download useful tools. I have a set of masked file...
• DEPRECATED tools in Galaxy
  Hi, Nearly most of the tools have been listed under "DEPRECATED" in Galaxy main instance (https:/...
• How to import a published workflow from a Galaxy server to my server?
  Hello, I would like to try to use published workflow. I found a list [here][1]. I can either "i...
• Search The Galaxy!
  Hello all, I am happy to announce that Galaxy now has several Google Custom Searches that make i...
• Question About Aachange Tool.
  Hello, Recently i have used galaxy to find corresponding amino acids to a list of SNPs that i hav...