Hello Mark,
Correct - no needed. Any Illumina data that results from a CASAVA 1.8 or
higher pipeline is already has quality scores scaled to Sanger Phred
with an ASCII offset of 33. This translates to the ".fastqsanger" format
in Galaxy, so no grooming is required, you can just assign the datatype.
How to do that is in the first link below. And all the details,
including how to read a FastQC report to determine this is in the
screencast.
Thanks!
Jen
Galaxy team
On 12/13/13 8:58 AM, Mark Lindsay wrote:
Hi James
do you need to run the Groomer on the latest Illumina data?
BW
Mark
On 13 Dec 2013, at 16:53, Jennifer Jackson <[email protected]
<mailto:[email protected]>> wrote:
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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--
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http://galaxyproject.org
___________________________________________________________
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
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