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

ADD COMMENTlink 5.3 years ago Parham ♦ 1.4k • updated 5.3 years ago Kamil ♦ 1.9k
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Thanks! So if my library is single-end does it mean that the library is unstranded?!

ADD REPLYlink 5.3 years ago
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