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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