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  • Gene ID in cuffmerge

    Hi everyone
    I have a question on IDs in cuffmerge output. I am doing cufflinks with -g annotation.gtf file. gene_id and transcript_id seem correspond to the gtf file.

    2L Cufflinks exon 7529 8116 1 + . gene_id "FBgn0031208"; transcript_id "FBtr0300689"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.001241"; cov "0.000000";
    2L Cufflinks exon 8193 9484 1 + . gene_id "FBgn0031208"; transcript_id "FBtr0300689"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.001241"; cov "0.000000";

    But to run cuffdiff I run cuffmerge first. Then the ids are changed to cufflinks id, which looks like (although I still used the -g option):
    2L Cufflinks exon 7529 8116 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "CG11023"; oId "FBtr0300690"; nearest_ref "FBtr0300690"; class_code "="; tss_id "TSS1"; p_id "P1";
    2L Cufflinks exon 8193 8589 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "CG11023"; oId "FBtr0300690"; nearest_ref "FBtr0300690"; class_code "="; tss_id "TSS1"; p_id "P1";

    As result when I used this merged gtf file to run cuffdiff, ids still remain in this format...

    I am running everything with annotation gtf file when -g option is available so I am not sure why this is still happening.
    Thanks for help in advance.

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