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• How To Decide "Mean Inner Distance Between Mate Pairs"?
  Dear All, I am analyzing the downloaded RNA-seq datasets. However I am not sure how much is Mean...
• Picard tool collect insert size metrics not working
  Hi,   I am a newbie to RNA Seq analysis and Galaxy. I was trying to calculate the mean inner di...
• How to set 'mean inner distance' for paired-end reads?
  Hi all, If I use Paired-end sequences for 'Tophat for illumina' or 'Tophat 2', I need to type in...
• Tophat "Mean Inner Distance Between Mate Pairs"
  Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in "Mean Inner Distanc...
• Insert sizes in Galaxy
  I am new to RNASeq analysis. I used tophat to generate BAM files from FASTQ files but in the para...
• Error Running The Picard Tool?
  Hi, I am trying to determine the mean inner distance between mate pairs, but encountered odd resu...
• Can I Convert Paired-End Datasets Into Single End Ones?
  Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inn...
• Mean Inner Distance
  Hi Vanessa, Mean inner distance can be thought of as being the estimated gap left between the tw...
• Tophat can run negative r
  Regarding to Mean Inner Distance between Mate Pairs, I tried run ~1000000 reads twice: (1) if r...
• Run Bowtie To Estimate Mean Inner Distance Between Mate Pairs
  Dear All, In order to figure out the Mean Inner Distance between Mate Pairs of my paired-end RNA...
• Cuffdiff Errors: "Loading reference annotation" and "Inspecting maps and determining fragment length distributions". whats that mean?
  Hello everybody, I'm very new in RNA seq analysis I have run cuffdiff on 3 condition dataset coll...
• Generate SQ Lite database for cummeRbund not working with CuffDiff, and other general questions
  Hi everyone, I am currently a final year undergraduate studying at UoM set with the final yet pr...
• This job was terminated because it used more memory than it was allocated
  Hello, I have always encountered such problem "This job was terminated because it used more memo...
• Illogical Results In Tophat2 Analysis
  Hello, I used a Tophat 2 analysis and got 99.2% discordant in the summary, while in fact I chec...
• Bwa And Fastq Joiner Issues
  Hello, I hope someone might be able to help me with these issues, as I'm relatively new at Bioin...
• Number Of Mismatches Allowed In The Initial Read Mapping
  Dear All, I tested how to set the "Number of mismatches allowed in the initial read mapping" a...
• Problem running Clustal 2.1 Multiple Sequences Alignment - an instance of 'std::bad_alloc'
  Dear All, I've been trying to analyze reads from a short transcript. The data I have was obtaine...
• How To Process Paired Reads In Galaxy
  Hi Users How do I process paired reads from an Ilumina Miseq platform? If I first use "Groomer" ...