Hi Jianguang, No, multiple transcripts can share this identifier, but it does represent a transcript group. See the Cuffdiff output file "transcript FPKM tracking" for the mapping and the unique transcript identifiers w/ other related keys, coordinates, etc. A description of this file and all Cuffdiff output files is in the Cufflinks manual here: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output Hopefully this helps! Jen On 8/24/12 12:15 PM, Du, Jianguang wrote:

Dear All,

I am reading and comparing the outputs of Cuffdiff. I found there is a "tss_id" column in "transcript FPKM tracking", "gene FPKM tracking", "TSS groups FPKM tracking" and "CDS FPKM tracking" files. In this column, each line has a unique label such as "TSS1001". This kind of labels also appear under "test_id" column in "TSS groups differential expression testing" and "splicing defferential expression testing" files. Does each of this kind label represent a unique transcript? In other word, does each transcript has a unique label initiating with TSS followed by numbers?

Thank.

Jianguang

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