What is my RNA-seq data's library-type?!

Question

[Parham]

Hi,

I know it's a typical question but I couldn't figure it out reading forums and manual. So I have to set this library-type for TopHat but I don't know how to find what is my library-type! I just checked the accepted_hits.bam out of TopHat in IGV and Color aligned by read strand, here is an screenshot but I am not sure if it is telling anything regarding the library type! Any advise on this is appreciated.

Answer 1

[Kamil]

Please see:

• http://onetipperday.blogspot.com/2012/07/how-to-tell-which-library-type-to-use.html
• http://cufflinks.cbcb.umd.edu/manual.html#library

Related questions:

• Tophat Library Type And Pair Orientation For Illumina Data

[Parham]

Thanks! So if my library is single-end does it mean that the library is unstranded?!

[qin.tang]

I have the same confusion! Have you found the answer? Could you share it? Many thanks!