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• Need help with "Call SNPS with Freebayes" tool
  Dear Galaxy team how to put reference file in Call snps with freebayes and is it used in RNA seq...
• plotting multiple bigwigs in agregate plots
  What's the right tool to plot multiple bigwigs around a reference point like TSS? Can you help me...
• Extract SNPs flanking sequence from organisme without reference genome
  Hi, I'm new in managing DNA sequences and I'm looking for help. I have fastq and vcf files from t...
• Regrading Snps
  I wish to compare SNPs in my mouse sample (SNP file generated from Partek Genomic suite) with SNP...
• Question About Plotting Circos Plot
  I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g ...
• How To Extract Geneid From Pileup File?
  Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. ...
• plotProfile/plotHeatmap - How to change the file names?
  I would like to compare H3K4me3 ChIP peaks of several samples at TSS. Therefore, I used "compute...
• Overlapping axis labels when graphing quality score box plot
  Hello~ Small SOS. I'm trying to graph the quality box plot and the nucleotide distribution chart...
• Multiple fastq file for mapping with Bowtie2
  Hi,   I have some amplicon sequences for 144 samples that I would like to map on to a reference...
• Extracting All Cpg-Snps From Dbsnp135
  Dear Sir / Madam, I'm new to Galaxy. Is there any way to extract all CpG-SNPs from dbSNP135 usin...
• Problems in SNPs identification
  Hello   I am Viva I am using galaxy as a platform to identify SNPs in my datasets. I have two d...
• multiBamSummary in DeepTools_sample order did not match to the entry
  Hi Everyone, I tried to plot the correlation plots using the DeepTools on the web base Galaxy. ...
• Re: Question From Ucsc About Snps And Proteins
  Hi Jen, "Mutate Codons with SNPs" tool under "Evolution" section on Galaxy should help to answer...
• Galaxy cummeRbund fails to identify sample name for X and Y axis for scatter and volcano plot
  Hello, I have cuff diff sqlite db for 2 samples and I wish to visualise the result using galaxy-c...
• How to know if mapping to reference genome was succesful?
  Given a set of BAM files for single-end reads just mapped with BWA tool, how can I have an overvi...
• Hg17-->Hg18 Liftover Problem
  Hi folks, I am trying to perform a liftover of a UCSC wiggle plot from hg17 coordinates to hg18...
• Snippy does not recognize my genbank reference file
  Hi, I'm using snippy to look for SNPs in my bacterial genomes. Snippy does not seem to be able t...
• An Error In Reporting A Tool Error...
  Hello all I am working with the LefSe module. Over the last two days, I am gettimg a recurring er...
• Tool to catalog SNPs
  Is there a way in which I can catalog SNPs on Galaxy? I am attempting to use my BAM file, along w...
• How to separate SNPs from other variant types in Galaxy?
  I have a VCF file with all the called variants. I want to keep just the SNPs. This is achievable ...