Re: [galaxy-user] CuffDiff gene fpkm tracking file.
> > 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_01 - - MT-ND5 - chrM:0-1657112484.2 > 12260.8 12707.7 11447 11233.1 11661 > XLOC_02 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 > 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 > XLOC_03 - - 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_04 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 > 3.98118 0 7.99721 4.62875 0.2785198.97899 > > I this is normal, how can I find the class code of transcript listed in the > CuffDiff gene expression file? > 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. ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
[galaxy-user] CuffDiff gene fpkm tracking file- Sorry! I sent only a part of my email
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_01 - - MT-ND5 - chrM:0-1657112484.2 12260.8 12707.7 11447 11233.1 11661 XLOC_02 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 XLOC_03 - - 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_04 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.2785198.97899 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. ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
[galaxy-user] CuffDiff gene fpkm tracking file.
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_01 - - MT-ND5 - chrM:0-1657112484.2 12260.8 12707.7 11447 11233.1 11661 XLOC_02 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 XLOC_03 - - 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_04 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.2785198.97899 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. ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
