I have RNA-seq data that I want to map using TopHat. The library prep was done using ScriptSeq v2, and the sequencing using Illumina.
The R1 sequences the sense cDNA from start to finish. The R2 sequences the antisense cDNA from finish to start.
The --library-type option fr-unstranded says that "Reads 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.", which would seem to be just what I need.
However how does it deal with sense cDNA that has been expressed from the negative strand of the DNA? If an R1 read is just that, then wouldn't the read have to be reversed to map to the genome?
Has anyone dealt with anything similar, and if so, do you know which settings I should use for TopHat?
The R1 sequences the sense cDNA from start to finish. The R2 sequences the antisense cDNA from finish to start.
The --library-type option fr-unstranded says that "Reads 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.", which would seem to be just what I need.
However how does it deal with sense cDNA that has been expressed from the negative strand of the DNA? If an R1 read is just that, then wouldn't the read have to be reversed to map to the genome?
Has anyone dealt with anything similar, and if so, do you know which settings I should use for TopHat?
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