Tweet
Hi all,
I want to use Tophat to map reads to the reference genome such that it just reports reads that are mapped only to one positive exactly. This means that if a read is mapped to 2 or positions, this read will be discarded.
I found the (-x) option in tophat "Maximum number of mappings allowed for a read". So, I can set it to (1) but, as per the description of this option, I am afraid that it is applied only to reads being mapped to the provided transcriptome. What about novel reads that do not match the transcriptome? (i.e. why this option is linked to the -G option?).
I want to use Tophat to map reads to the reference genome such that it just reports reads that are mapped only to one positive exactly. This means that if a read is mapped to 2 or positions, this read will be discarded.
I found the (-x) option in tophat "Maximum number of mappings allowed for a read". So, I can set it to (1) but, as per the description of this option, I am afraid that it is applied only to reads being mapped to the provided transcriptome. What about novel reads that do not match the transcriptome? (i.e. why this option is linked to the -G option?).