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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