This example is the current default setting. Only the map4 module is used.

tmap mapall ? -f /results/referenceLibrary/tmap-f3/hg19/hg19.fasta -r /<server_path>/results/analysis/output/Home/Auto_user_G35-685--R65832-110mM_K2SO4-OT_salts-0630_24057_58335/IonXpress_057_rawlib.bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4

This example is the previous TMAP default. This example uses the modules map1, map2, and map3, in that order. Progressively more reads are mapped by each module.

tmap mapall  f <FASTA_file> -v -Y -u --prefix-exclude 5 stage1 map1 map2 map3