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Question: Cuffdiff Gene Fpkm Tracking File.
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gravatar for Samuele Gherardi
7.8 years ago by
Samuele Gherardi • 20
Samuele Gherardi • 20 wrote:
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.
rna-seq cuffdiff • 2.0k views
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modified 7.8 years ago by Jeremy Goecks • 2.2k • written 7.8 years ago by Samuele Gherardi • 20
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gravatar for Jeremy Goecks
7.8 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Hi Samuele, Without seeing your history, it's difficult to say for certain what your problem is. However, I'd guess that the GTF file that you're providing to Cuffdiff does not have the p_id attribute. You can produce a GTF file with both tss_id and p_id attributes by running Cuffcompare and using sequence data. Thanks, J.
ADD COMMENT • link written 7.8 years ago by Jeremy Goecks • 2.2k
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