Setting up GMAP for EST mapping

Question

[endretoth]

Hi,

I would like to set up GMAP for the following criteria (if it is possible, if not something similar). I have about 280,000 EST and I would like to map them on a genome.

• coverage>=90%
• identity>=90%
• best path(match)

so far, my command in unix looks like:

gmap -D Genom_database/ -d Genom_database -B 5 -A -t 4 EST_all.fasta -f gff3_gene --cross-species

I would like to request help, which options should I give to GMAP to achieve the above mentioned criteria (I'm not an expert in GMAP).

I greatly appreciate any help! :)

Answer 1

[lieven.sterck]

did you look into the manual of GMAP? (or even the build-in help?)

doing so I got the following options:

  --min-trimmed-coverage=FLOAT   Do not print alignments with trimmed coverage less
                                   this value (default=0.0, which means no filtering)
                                   Note that chimeric alignments will be output regardless
                                   of this filter
  --min-identity=FLOAT           Do not print alignments with identity less
                                   this value (default=0.0, which means no filtering)
                                   Note that chimeric alignments will be output regardless
                                   of this filter

I did not look into detail but they sound promising.

one other tip I van give: have a look at the GenomeThreader software. Much more performant, quicker, accurate, ... Moreover it has multiple options to do all sorts of filtering of the results