TMAP examples

This example uses TMAP map4 mapping algorithm with default settings.

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

The next example is the previous TMAP default setting. This example uses the map1, map2, and map3 modules 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