lel.eory at ed.ac.uk
Fri Aug 2 09:50:26 BST 2013
I try to identify low complexity regions for some species by running the
ensembl 'dust' analysis pipeline.
file does not contain configuration section for logic_name 'dust'. Can
someone possibly give me the configuration corresponding to dust? (Grid
engine parameters would be a bonus.)
The cvs_checkout/ensembl-doc/pipeline_docs/the_raw_computes.txt file
says that the source for dust is coming from the NCBI blast suit (see.
module description, line 245) and the "Analysis conf" section name the
program as tcdust (same file line 573), which is consistent with the
analysis tables from the databases. Is tcdust available to download from
somewhere? (The NCBI blast+ package only have dustmasker, but no tcdust.)
If not can someone possibly print out the detailed help from tcdust and
e-mail it back, if such a help exists for tcdust, to understand the
various parameters the program accepts?
From Dust.pm I assume the output goes to STDOUT and has the format of
START..END - where START/END is the start and end coordinates of the
low-complexity region - is this correct?
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