Dear all,
according to FIMO guidelines the option --max-stored-scores
Set the maximum number of scores that will be stored. Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate.
the default behaviour is
The maximum number of stored matches is 100,000.
Now i would like to know:
* how many scores were kept during my analysis
* how is possible to know if what they say (dropping 50% of the scores in the case they exceeded the max allowed) happened behind the scenes.
here the code i'm running (i''ve set the --max-stored-scores so big just in case): fimo --bfile background_model.txt --qv-thresh --max-stored-scores 20000000 --thresh 5e-2 motifs.meme promoters.fa
