how to get the transcription start site?

[caiji-lh]

Hi, Dr. Wang,

1. I want to get the information of transcription start site in the output file. I tried many parameters and failed. How should I get this information?
2. I annotate the information of the CpG island through the "cpgIslandExt.txt". I want to add the location information of the corresponding CpG island in the output file.

[kaichop]

I did not understand the question so did not reply. Is the problem resolved? The gene-annotation output should have something like c. and p. which means the start site of mutation within the transcripts or translated proteins.

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