Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: what type of library to choose in set advanced cufflink option
0
gravatar for 1603.neha
2.6 years ago by
1603.neha • 70
1603.neha • 70 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 COMMENT • link •
modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by 1603.neha • 70
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.6 years ago by 1603.neha • 70
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour