I'm generating paired-end reads experiments.
with the option UNIQUE_IDS = YES I generate strand-specific data
while with the option UNIQUE_IDS = NO I generate not- strand specific.
Am I right?
the UNIQUE_IDS flag does not influence the sequencing process itself. It only ensures that the ID's generated by the simulator are unique and can be processed easily by other tools. In order to achieve that, if the flag is set to YES, the sense information (A or S) is not added to the read id but encoded in the pair information. In that case /1 reads are always sense reads while /2 reads are always anti-sense.
You can get more information about the parameters by executing
this will print all available parameters and their descriptions:
# 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.
# true|false or yes|no default: false
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