hi i have performed QC then groomer then tophat on SRA sequences which were single end. now i want to run cufflink. want to know what should i choose in advance cufflink option in library prep used fo rinput reads. as the sra id give sonly information of being cdna or genomic. ff and fr list of options i cant understand. please explain
Basic NGS data types and source library construction methods are covered here: https://wiki.galaxyproject.org/Learn/GalaxyNGS101
More about what these terms mean to Cufflinks is in the manual here: http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html
In short, the library type should match the library prep and read orientation. If that is an unknown, you could try contacting the data authors or reviewing the related publication for the data (if there is one).
Best, Jen, Galaxy team
dear jen i have checked this link earlier also but it doesnt solve my problem. the advance option in cufflink asks about library type- ff-unstranded, fr-unstranded or stranded .these details are not available in data and paper also. i request if you can again look into it.