Option -categorize in SNAP gene prediction.

Question

[Picasa]

Hi,

I am starting a genome annotaiton using SNAP for gene finder. I'am confused about this command:

fathom genome.ann genome.dna -categorize 1000

I am not sure to understand what is the 1000.

Based on the manual, it means:

Categorizes genomic regions into those that contain errors (err), warnings (wrn), alternate forms (alt), overlapping genes (olp), and unique genes (uni). Typically, only the unique genes are used for training and testing. The value of "i" limits the intergenic sequence at the ends.

But I still don't understand. I will be grateful for your help.

Thanks

Answer 1

[janneke.aylward]

This is quite an old question, but for anyone else that may be interested:

The integer after -categorize (similarly, the one after -export) refers to the length (in bp) of flanking sequence that will be included. I think that is also what you are referring to with the value of "i".

See https://www.psc.edu/user-resources/software/snap/detailed-information