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1.       What are the differences between Flux Capacitor and Flux Simulator?

2.       I specified the .PRO file in Flux Capacitor as below:

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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:

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                [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)?

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  1. Hi,

    The READ_DESCRIPTOR value STRAND_MATE expects read IDs of the form

         <ID>"/"[0-2]"/"[1-2]

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    mapSimpleDescriptors.put(DESCRIPTORID_STRAND_MATE, 
    SYMBOL_TAG_LEFT+ TAG_ID+ SYMBOL_TAG_RIGHT+
    "/"+
    SYMBOL_TAG_LEFT+ TAG_STRAND+ SYMBOL_TAG_RIGHT+
    SYMBOL_SET_LEFT+ "0,1,2"+ SYMBOL_SET_RIGHT+
    "/"+
    SYMBOL_TAG_LEFT+ TAG_PAIR+ SYMBOL_TAG_RIGHT+
    SYMBOL_SET_LEFT+ "1,2"+ SYMBOL_SET_RIGHT);

     

    Alternatively, there is a value SIMULATOR for the parameter READ_DESCRIPTOR, which expects <ID> ":"[S,A]"/"[1-2] as an equivalent for stranded and paired reads:

     Click here to expand...
    mapSimpleDescriptors.put(DESCRIPTORID_SIMULATOR, 
    				SYMBOL_TAG_LEFT+ TAG_ID+ SYMBOL_TAG_RIGHT+
    				":"+
    				SYMBOL_TAG_LEFT+ TAG_STRAND+ SYMBOL_TAG_RIGHT+
    				SYMBOL_SET_LEFT+ "S,A"+ SYMBOL_SET_RIGHT+
    				"/"+
    				SYMBOL_TAG_LEFT+ TAG_PAIR+ SYMBOL_TAG_RIGHT+
    				SYMBOL_SET_LEFT+ "1,2"+ SYMBOL_SET_RIGHT);

    You should check also the Simulator Parameter UNIQUE_IDS: If set to TRUE, the simulator will NOT add sense/anti-sense information to paired reads (not A/S is appended to the read ID) in order to create unique ids paired end ids where the only difference is the /1 /2 at the end of the ID. To keep track of orientation, /1 is always used for sens reads, while /2 is always appended to anti-sense reads.

    Currently, this parameter is deactivated in the default settings. However, if switched on, a READ_DESCRIPTOR of MATE1_SENSE might be more appropriate.

     

    I hope my explanations help you, best wishes!