I have some questions about read orientation in Tophat for Illumina data that I cannot find the clear answers yet and I hope you can shed some light on these.
1 Does the fr in [fr-unstranded,fr-firststranded, fr-secondstranded] correspond to forward-reverse? I wonder whether paired end read orientation can be set for Tophat.
2 According to description about library type, "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." does left-most end of fragment in transcript coordinates correspond to the read in first first file in paired-end data?
3 Some of public data that I collected do not have information about library type except only platform (standard illumine or strand specific Illumina), can I assume that they are fr-unstranded and fr-secondstrand respectively?
1 Does the fr in [fr-unstranded,fr-firststranded, fr-secondstranded] correspond to forward-reverse? I wonder whether paired end read orientation can be set for Tophat.
2 According to description about library type, "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." does left-most end of fragment in transcript coordinates correspond to the read in first first file in paired-end data?
3 Some of public data that I collected do not have information about library type except only platform (standard illumine or strand specific Illumina), can I assume that they are fr-unstranded and fr-secondstrand respectively?
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