I'm using sga only for scaffolding (I already have a genome assembly performed with another software). I have two libraries: a paired-end library (oriented as default orientation; FR) and also a mate-pair library, which was preprocessed with NxTrim, which apart of removing PE contamination from raw reads, it also changes by default the orientation of the reads. Thus, my clean MP reads are in FR instead of RF.
I'm worried because in https://github.com/jts/sga/wiki/Scaffolding-multiple-libraries I understand that if FR > RF, then the scaffolding from MP could not improve. However, I assume that is only a question of being or not PE contamination rather than a strict problem of orientation. So, my question is: if my MP reads are free of PE contamination but they are in FR instead of RF, it could be problematic for sga scaffolding? If so, there is any option in the program to solve this or it is mandatory to change the orientation of FR to RF?
Thanks,
Dear supporting team,
I'm using sga only for scaffolding (I already have a genome assembly performed with another software). I have two libraries: a paired-end library (oriented as default orientation; FR) and also a mate-pair library, which was preprocessed with NxTrim, which apart of removing PE contamination from raw reads, it also changes by default the orientation of the reads. Thus, my clean MP reads are in FR instead of RF.
I'm worried because in https://github.com/jts/sga/wiki/Scaffolding-multiple-libraries I understand that if FR > RF, then the scaffolding from MP could not improve. However, I assume that is only a question of being or not PE contamination rather than a strict problem of orientation. So, my question is: if my MP reads are free of PE contamination but they are in FR instead of RF, it could be problematic for sga scaffolding? If so, there is any option in the program to solve this or it is mandatory to change the orientation of FR to RF? Thanks,
Edu