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
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