1. What are the differences between Flux Capacitor and Flux Simulator?
2. I specified the .PRO file in Flux Capacitor as below:
ANNOTATION_FILE some_gtf_file.gtf
COUNT_ELEMENTS [SPLICE_JUNCTIONS, INTRONS]
ANNOTATION_MAPPING AUTO
MAPPING_FILE my_bed_file_for_sample1.bed
PROFILE_FILE output_dir
STATS_FILE output_dir
STDERR_FILE output_dir
STDOUT_FILE output_dir
READ_DESCRIPTOR STRAND_MATE
However, when I run flux-capacitor -p par_file.par, the following errors appear:
[ERROR] Read Descriptor {ID}/{STRAND}[0,1,2]/{MATE}[1,2] incompatible with read IDs
java.lang.RuntimeException: Read Descriptor {ID}/{STRAND}[0,1,2]/{MATE}[1,2] incompatible with read IDs
at barna.flux.capacitor.reconstruction.FluxCapacitor.fileStats(FluxCapacitor.java:2847)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1798)
at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
at barna.commons.launcher.Flux.main(Flux.java:198)
My questions are: what should I input for READ_DESCRIPTOR? Also, for COUNT_ELEMENTS, are the only options SPLICE_JUNCTIONS and INTRONS? What are the output files for Flux Capacitor?
3. Will any of the Flux Capacitor output files directly useable in Flux Simulator (in its .PRO file, I guess)?