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• bam to stranded bigwig?
  Hi, I have a bam file generated from stranded RNA-seq data - is it possible to use galaxy to spli...
• Split barcodes tool
  Hello,     I am trying to use the split barcodes tool in Galaxy. For some reason, it does not se...
• RNA-seq analysis in Galaxy
  I am doing RNA-seq analysis for several mouse samples and I encounter problems during differentia...
• Need Help To Split Paired-End Dataset
  I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial...
• SAM Split tools only generate one split data
  Hi there, I'm using Galaxy to analyze my ChIP-seq data, but when I use NGS: SAMtools → Split to ...
• splitting and rejoining datasets
  I am working with large fastq files which are too big to use on galaxy (about 120 gb, so even aft...
• (No Subject)
  I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial...
• filtering pair-end bam file
  Hello, I am trying to filter a pairend bam file to get only forward reads in Galaxy. A bam filter...
• FASTQ file split (forward and reverse not of same length)
  Is there a Galaxy package which will split a previously joined fastq which will have unequal forw...
• Tophat Paired End Read
  Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping...
• Merging Fastq Files
  Hi I have received Illumina paired-end genome sequence data as a .tar file. When unpacked the dat...
• how to get multiple bam files generated by bam split in Galaxy local
  Hi, I want to add a small tools using bam to my local Galxy server.if i run this command on linu...
• How do I down sample a fastq in Galaxy?
  I want to make a small fastq file for testing and demonstration proposes.  On the command line I ...
• Split VCF file
  I would like help splitting a large vcf file containing WGS data into smaller files. Using Gala...
• Convert multiple FASTQ files into one BAM file
  Hello guys! I recently started working with NGS analysis and I may have a stupid question to ask....
• File Extensions
  One issue I have stumbled upon is that the tmp files fed into the program do not preserve the fil...
• Waiting to run for 6 days
  I submitted 6 fastq files to be aligned using Tophat 6 days ago. 5 were aligned within 24 hours. ...
• SAMtools Merge BAM files hangs
  Hi all, I am using TopHat to map RNA-seq reads. My study species is a non-model organism, so I c...
• Insert sizes in Galaxy
  I am new to RNASeq analysis. I used tophat to generate BAM files from FASTQ files but in the para...
• fastq splitter problem
  fastq splitter is not working on paired end read for some of my file and produce output file with...