Question: what type of library to choose in set advanced cufflink option
gravatar for 1603.neha
2.6 years ago by
1603.neha70 wrote:

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

tophat sra rnaseq cufflink • 1.0k views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by 1603.neha70
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Basic NGS data types and source library construction methods are covered here:

More about what these terms mean to Cufflinks is in the manual here:

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

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k

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.

ADD REPLYlink written 2.6 years ago by 1603.neha70
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