Hello, of course, Jennifer is right for the first question 😊 . For the second 
question about  blast ... I wonder if running after blast in galaxy I can 
remove sequences that can contaminate the data. It's possible?

Last question, trinity is 100% operational in galaxy? Because trinity ran but 
the result was empty, and I think the script failure .Py

Thanks Jennifer and colleagues for your patience and solutions

Date: Fri, 13 Dec 2013 08:53:31 -0800
From: j...@bx.psu.edu
To: braun_...@hotmail.com; galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] fastqc and blast?


  
    
  
  
    Hello,

    

    For the first question, make sure that you are running the groomer
    with the correction options. In almost all cases for Illumina data
    this will mean leaving all but one setting at default. The setting
    to change is "Input FASTQ quality scores type:". The results of
    FastQC will inform you about how to set this. An example is in this
    wiki section's screencast plus the first bullet point:

    https://wiki.galaxyproject.org/Support#Dataset_special_cases

    http://vimeo.com/galaxyproject/fastqprep

    

    For the second, I am not sure what you mean by 'different'. Do you
    mean the data may have contamination from another species? Or that
    the the data content may be different with respect to quality? 

    

    In short, to filter based on quality as reported in the FastQC
    report, try tools in the same tool group such as "FASTQ Trimmer" or
    "FASTQ Quality Trimmer". 

    

    The protocols included in our RNA-seq pipeline help start out with
    some quality steps:

https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq

    

    And many from our community have contributed RNA-seq tutorials:

    https://wiki.galaxyproject.org/Learn#Other_Tutorials

    

    Hopefully this helps!

    

    Jen

    Galaxy team

    

    
    On 12/13/13 7:05 AM, Jorge Braun wrote:

    
    
      
      Hello
          mates,

          

          I have two doubts
          galaxy:

          

          a) I have rna-seq data
            from Illumina and do fastqc ... the results are good but
            when I fastgroomer to Sanger format and then fastqc
          ... the results
            are bad. Does anyone
            know the cause? I do not understand
            why.

          

          b) With
          the same sequences can
          know if they are different
          Rna and eliminate
          those that do not want
            to examine?

          

          merry christmas :)
      
      

      
      

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    -- 
Jennifer Hillman-Jackson
http://galaxyproject.org                                          
___________________________________________________________
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