Questions about Cuffmerge and Cuffdiff

[pbluescript]

GTF files are one based.
There is not sufficient information to provide an answer for your second question. Your best bet would be to load up the reads in something like IGV and actually look at the region in question to see where they are mapping.

[aquleaf]

Hi all.

I have two questions about Cuffmerge and Cuffidiff.

1, Is the merged gtf file generated by Cuffmerge 0-based or 1-based?

2, How to understand more than one reference genes are associated with a Cufflinks gene locus in the gene_exp.diff file?
For example,

test_id    gene_id    gene    locus    sample_1    sample_2    status    value_1    value_2    log2(fold_change)    test_stat    p_value    q_value    significant
XLOC_000006    XLOC_000006    CG11455,CG3436,spen    2L:114725-203492    w    sa    OK    226.12    124.924    -0.856039    0.038781    0.969065    0.999964    no

Should I discard this record because more than one reference genes were associated? However, some transcripts of one or two of the reference genes,e.g.CG11455, were demonstrated to be differentially expressed in the isoform_exp.diff file.

Wish help! Thanks very much in advance!