FPKM is 0, when using cufflinks in galaxy on the net

[chenyao]

Dear all,

I have a problem when using cufflinks in galaxy (net version). If I didn't select the reference annotation, I can get the FPKM values,but since no reference,I can not get the transcript or gene name. It looks like these:

test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant
TCONS_00000002 XLOC_000025 - chr1:33860011-33860048 q1 q2 NOTEST 1.794e+06 0 -1.79769e+308 -1.79769e+308 0.0188163 1 no

There is no gene_id. However, if I use the reference annotation downloaded from ENSEMBLE.I can get the gene_ids, but there FPKM values are all "0":

tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status FPKM FPKM_conf_lo FPKM_conf_hi
ENSMUSG00000024232 - - ENSMUSG00000024232 Bambi - 18:3507954-3516402 - - OK 0 0 0
ENSMUSG00000091539 - - ENSMUSG00000091539 Vmn1r238 - 18:3122454-3123465 - - OK 0 0 0

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Any thoughts?

[jmh175]

I have had this problem as well. You need to look at your annotation file (Im assuming its GTF or GFF3 file format) and make sure that the first column, which denotes what the chromosome is, matches the name for the reference file you used in your initial alignment.