Question: Cuffdiff Gene Fpkm Tracking File- Sorry! I Sent Only A Part Of My Email
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Samuele Gherardi • 20 wrote:
Hello everybody,
I'm quite new in NGS world, I'm trying to analize dome RNA-seq data. I
followed the workflow through tophat,cufflink,cuffcompare and cuffdiff
I suppose everything work fine but in the Cuffdiff gene fpkm file the
column Class_Code is empty and i don't know why?
this is an example of my CuffDiff gene fpkm tracking file.
tracking_id class_code nearest_ref_id gene_short_name tss_id
locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo
q2_conf_hi
XLOC_000001 - - MT-ND5 - chrM:0-16571
12484.2 12260.8 12707.7 11447 11233.1 11661
XLOC_000002 - - USP14 TSS1,TSS2,TSS3
chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368
27.1371
XLOC_000003 - - SMCHD1
TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540
28.2493 17.5093 38.9892 27.2263 16.6263 37.8262
XLOC_000004 - - EMILIN2 TSS13,TSS14
chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.278519
8.97899
I this is normal, how can I find the class code of transcript listed
in the CuffDiff gene expression file?
thank you in advance
Samuele.