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• 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...
• 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. ...
• ChIP seq Motif analysis
  Hi, How to do motif analysis after peak calling? I used MACS2 for peak calling, used fastq to fa...
• Motif discovery-Chip seq
  Hello, I am analyzing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads wi...
• Motif Search from Bed file
  Hi all, I have recently generated a list of motifs of TF binding sites within peaks of my ChIPse...
• FIMO motif search
  Hi all, I would like to use FIMO motif search tool provided by usegalaxy.org to scan a list of ...
• conversion to Bedgraph files
  Hi, I have BAM files from Bowtie2. I want to use MACS2 bdgdiff in galaxy to identify differntial...
• Counting number of times multiple defined values appear in the dataset
  I have gotten SNP data on a number of regions via UCSC genome browser. I have assigned all SNPs w...
• Repeat identifer in genomic sequence
  Is there an option in galaxy to identify repeat motifs?  The track tandem repeat finder, also cal...
• How To Get Random Region Of 1000-Bp Window In The Chromosome Not Overlapping Specific [Gtf] File
  Dear Galaxy develop team: As the subject said, I need to obtain random regions which are 1000-b...
• 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. ...
• Has the operate on genomic intervals - intersect feature been removed?
  Hello, The intersect tool under "Operate on Genomic Intervals" has suddenly disappeared.  Is thi...
• 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...
• Homer for Motif search
  Hi,    I would like to use HOMER to search for enriched motif on a ChIPseq analysis I did using ...
• How to identify the SiRNA abundance from transcriptome data
  Hi all, I am having transcriptome data of c.elegans i would like to analyse the differential exp...
• Extract identifiers from collection in tool XML
  If I have a collection of files, how would I extract the identifiers in an XML to pass it into an...
• Alignment Coordinates
  Hello, I imported a sequence alignment file from clustalw. How can I generate a list of the coor...
• Downloads Maf Files
  Hi, I want to download MAF files for the exonic regions of the genome. Additionally I want the s...
• Output Files of MACS2 bdgdiff
  Hello everyone, I have some bedgraph files from a ChIP-Seq experiment (2 replicates for each cond...
• Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
  I am planning to use exogenous chromatin as a spike in control with my actual sample from mouse t...
• How to compare two libraries
  Dear Service, I load in Galaxy server about 10 histories. Each one is composed of a fastq file a...
• rearrange columns with Galaxy
  Hello, I have the following GFF file: ##gff-version 3 #!gff-spec-version 1.21 #!processor ...
• bedtools - shuffle with overlapping even if -noOverlapping option activated
  Hi everybody, After different tries, I realize one thing about the BEDtools tool ShuffleBED and ...
• How to judge the quantitativity of ChIPSeq?
  Hi, I have now been through my ChIP-Seq analyses with some success using the Galaxy platform up ...