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  • cuffdiff does not gene name

    Hi, all
    I am analyzing my data in Galaxy using bowtie2--cufflinks--cuffmerge--cuffdiff.
    I used the annotation gff file in the steps of cufflinks and cuffmerge.
    Now in the result of cuffdiff, I cannot find the gene names.
    My results in the sqlite file have such columns:
    gene _id sample_1 sample_2 status values_1 value_2 log2_fold_change test_stat p_value 1_value significant
    How can I let the result shows up gene name?
    Thank you!

  • #2
    update
    I just found the gff file I used does not have the column gene name though it has gene name described in the last column with other information.
    So, I think that is the reason

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    • #3
      update:
      I found a file of feature_table.txt has gene names. How can I convert the feature_table.txt file in to gtf or gff3 file?

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      • #4
        With the package rtracklayer for R it is quite easy. Import your table, make a GRanges object with the correct elementMetadata and then export in gtf...

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