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• 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...
• How To Find Out Snps And Point Mutations In Rna-Seq Data Using Galaxy?
  HI, I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy s...
• Extract assembled transcripts from Cufflinks gtf without to use reference genome
  Hi all, I know there were similar questions, but unfortunately I couldn't find proper answer for...
• Get Flanks skipped invalid lines
  Hello Galaxy Experts I have a query regarding "Get flanks" tool under "Operate on genomic inter...
• Workflow with collections
  The task was to download several SRAs from NCBI, align to reference genome, find SNPs. I made man...
• Rna Seq Analysis
  I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the ...
• Why I can't use some of the tools
  I have data from Illumina, as part1,fastq and part 2.fastq. First thing is that I want to join th...
• Variant analysis using Galaxy - tutorials, example workflows
  I have my FASTQ files, and I am trying to align them to the mouse reference genome, and perform v...
• SNP tool (Amino acid change) throwing error
  Hi I have discovered some 240,000 SNPs and am using the **"amino-acid changes caused by a set of...
• BAM file manipulations
  Hi I have made a whole assembly of RNA seq data using Trinity. The assembled file generated has ...
• Need help with Circos plotting of snps on Galaxy
  Please help me to make a Circos plot of snps against the reference genome on Galaxy. I have a bed...
• Stringtie "GffNameList Error: invalid index (-1)"
  Hello, I am doing some transcriptome assembly using Stringtie as well as other assemblers. I am r...
• Realigner Target Creator will not run?
  I have been running the pipeline below to try and call SNPs from RNA-Seq data but have encountere...
• Output files: "genome.*.bt2" file. What is it?
  Hi everyone, I ran Bowtie2, mapping my MiSeq reads against a plasmid (8kb) I had to find out if ...
• Problem with Reference genome from history in Tuxedo
  Hi, 1- I am using Tuxedo for tomato. I run the workflow from the shared data. In the TopHat sec...
• Need help with "MPileup" tool
  I am trying to get SNPs and indels from a bowtie 2 on Illumina reads matched to the sinorhizobium...
• Stuck
  I'm sure this is a silly question, but I have been stuck since yesterday. I have some whole genom...
• Trying to understand the steps for 'identify DNA polymorphism sites'
  Greetings! My partners and I got this homework. We're not specialized in bioinformatics or anythi...