Wednesday, June 5, 2013

How to tell which library type to use (fr-firststrand or fr-secondstrand)?

http://onetipperday.blogspot.ca/2012/07/how-to-tell-which-library-type-to-use.html


Tophat manual page has listed the general strand-specific protocol:
Library TypeExamplesDescription
fr-unstrandedStandard IlluminaReads from the left-most end of the fragment (in transcript coordinates) map to the transcript strand, and the right-most end maps to the opposite strand.
fr-firststranddUTP, NSR, NNSRSame as above except we enforce the rule that the right-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during first strand synthesis is sequenced.
fr-secondstrandLigation, Standard SOLiDSame as above except we enforce the rule that the left-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during second strand synthesis is sequenced.

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