Question: Subject: Analyzing Targeted Resequencing Data With> Galaxy
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Jackie Lighten • 20 wrote:
You can do all the quality filtering with Galaxy, but may involve
various
manipulations of the data. If I am not mistaken the "metagenomics"
workflow
may help you out a little. Its designed for 454 data but should give
you an
idea of how to go about things. There is a video tutorial on the site
for
this workflow.
A good place for you to start, however, may be here: Subject:
http://edwards.sdsu.edu/prinseq_beta/#
Prinseq is easy to use and will give you a full break down of your raw
data
and enables you to filter by quality/length etc.
FASTqc is an Illumina specialized preliminary analysis tool:
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
I my self was not very impressed with CLC at all. It lacks very
rudimentary
yet critical functions.
I am currently working on population amplicon data so couldn't really
help
you too much in the latest mapping to reference advances, but I found
the
Lasergene SEQman mapping and de-nova assembler much better than the
CLC
assembler.
Good luck
Jack
On 11