I got a quick question while using Flux Simulator: in the .PAR file, I need to provide several files, but I am not quite sure how to get them. Currently I assume:
REF_FILE_NAME: GTF annotation file directly downloaded from Ensembl?
PRO_FILE_NAME: results from Flux Capacitor?
LIB_FILE_NAME: not sure how to get this file…
SEQ_FILE_NAME: junctions.bed file from TopHat? How about insertions.bed and deletions.bed?
GEN_DIR: a directory containing .fa files of chromosome considered (say, Chr1 and Chr2)?
Thank you again for your kind help!