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Old 12-14-2015, 01:49 PM   #1
szy0931
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Default 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!
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Old 12-14-2015, 02:03 PM   #2
szy0931
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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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Old 12-14-2015, 02:42 PM   #3
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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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Old 12-14-2015, 11:28 PM   #4
SylvainL
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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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