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.
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Questions about Cuffmerge and Cuffdiff
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,
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.Code: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
Wish help! Thanks very much in advance!
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