Prediction of TSS from tuxedo pipeline

Question

[bioinfo_ga]

I have 22Million (150*2) human transcriptome reads. I have performed reference alignment using tuxedo pipeline (Tophat followed by Cufflinks).I need to calculate transcription start site (TSS) in my aligned transcripts and how to calculate position of TSS with respect to proximal and distant promoter.

Answer 1

[jnoble333]

I think in the case of a + strand transcript your TSS would be the leftmost position in exon 1 of the transcripts in the gtf file generated by cufflinks.