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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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RUM and multiple hits #167

Closed snandy3 closed 11 years ago

snandy3 commented 11 years ago

Hello,

I want to try "RUM" software to map reads but i have got a small doubt concerning multiple hits. If there are multiple positions for a read what is reported in the output file, all positions or just one of these ? I mean when a read can be mapped in different positions, i wanted to know if the software will return just one random position or will it return one of the best mapping position for this read. And is it possible with an option to have all the positions of that read ?

Advance thanks,

greggrant commented 11 years ago

Hi, yes, it can be set to return all positions. Just make sure to set the --no-bowtie-nu-limit option and it will do that. It can also be set to limit the number of locations to any desired number, however in that case the list returned is a random set of all possible. There is no preferencing of one position over another when something maps to multiple locations. Thank you, Greg

On Tue, 19 Feb 2013, snandy3 wrote:

Hello,

I want to try "RUM" software to map reads but i have got a small doubt concerning multiple hits. If there are multiple positions for a read what is reported in the output file, all positions or just one of these ? I mean when a read can be mapped in different positions, i wanted to know if the software will return just one random position or will it return one of the best mapping position for this read. And is it possible with an option to have all the positions of that read ?

Advance thanks,

Reply to this email directly or view it on GitHub: https://github.com/PGFI/rum/issues/167

snandy3 commented 11 years ago

Perfect thanks.