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!
Micha is drinking a Caipirinha at the beach, but maybe I can help you for the time being.
To run a standard simulation, you require a transcriptome annotation (REF_FILE_NAME, mandatory); optionall, for operations that require transcribed sequences, the genomic sequence is to be included (GEN_DIR).
The files PRO_FILE_NAME, LIB_FILE_NAME and SEQ_FILE_NAME are generated during the atomary steps of the pipeline; you do not have to provide these files for a usual run. An exception is the manual programming of the expression profile, where you provide a (partial) .PRO file (cf. ), precisely.