no XLOC gene_id or TCONS transcript_id in fpkm_tracking files

Question

[jolin0701-dy]

I run tophat (v2.1.0) -cufflinks (v2.1.1) for RNA-seq analysis.

In the output directory of cufflinks, there are 4 files: genes.fprkm_tracking isoforms.fpkm_tracking skipped.gtf transcripts.gtf

In genes.fprkm_tracking and isoforms.fpkm_tracking, there are only CUFF ids no XLOC gene_ids or TCONS transcript_ids.

I really need those ids to map back to Ensemble IDs and I am so sure that those ids were obtained from cufflinks output files.

Any help would be greatly appreciated~~~

$ head genes.fpkm_tracking 
tracking_id class_code  nearest_ref_id  gene_id gene_short_name tss_id  locus   length  coverage    FPKM    FPKM_conf_lo    FPKM_conf_hi    FPKM_status
CUFF.1  -   -   CUFF.1  -   -   1:3151345-3151390   -   -   3676.1  10.084  27.9249 OK
CUFF.2  -   -   CUFF.2  -   -   1:3151655-3151780   -   -   107.307 3.35099 10.3322 OK
CUFF.3  -   -   CUFF.3  -   -   1:3153069-3153260   -   -   38.8264 3.83785 9.13773 OK
CUFF.4  -   -   CUFF.4  -   -   1:3154020-3154070   -   -   2881.77 10.4718 29.3212 OK
CUFF.5  -   -   CUFF.5  -   -   1:3592898-3593185   -   -   8.0364  1.70274 4.62172 OK
CUFF.6  -   -   CUFF.6  -   -   1:3593240-3593449   -   -   16.9213 1.83717 5.67851 OK
CUFF.7  -   -   CUFF.7  -   -   1:3803226-3803292   -   -   480.831 2.6444  12.6931 OK
CUFF.8  -   -   CUFF.8  -   -   1:3984230-3985160   -   -   662.58  5.05886 15.6825 OK
CUFF.9  -   -   CUFF.9  -   -   1:3985230-3985282   -   -   1744.4  6.71272 20.8094 OK

$ head isoforms.fpkm_tracking 
tracking_id class_code  nearest_ref_id  gene_id gene_short_name tss_id  locus   length  coverage    FPKM    FPKM_conf_lo    FPKM_conf_hi    FPKM_status
CUFF.1.1    -   -   CUFF.1  -   -   1:3151345-3151390   45  3685.99 3676.1  10.084  27.9249 OK
CUFF.2.1    -   -   CUFF.2  -   -   1:3151655-3151780   125 103.065 107.307 3.35099 10.3322 OK
CUFF.3.1    -   -   CUFF.3  -   -   1:3153069-3153260   191 38.7774 38.8264 3.83785 9.13773 OK
CUFF.4.1    -   -   CUFF.4  -   -   1:3154020-3154070   50  2885.93 2881.77 10.4718 29.3212 OK
CUFF.5.1    -   -   CUFF.5  -   -   1:3592898-3593185   287 8.05801 8.0364  1.70274 4.62172 OK
CUFF.6.1    -   -   CUFF.6  -   -   1:3593240-3593449   209 16.8242 16.9213 1.83717 5.67851 OK
CUFF.7.1    -   -   CUFF.7  -   -   1:3803226-3803292   66  460.084 480.831 2.6444  12.6931 OK
CUFF.8.1    -   -   CUFF.8  -   -   1:3984230-3985160   69  614.535 662.58  5.05886 15.6825 OK
CUFF.9.1    -   -   CUFF.9  -   -   1:3985230-3985282   52  1749.09 1744.4  6.71272 20.8094 OK

Answer 1

[Satyajeet Khare]

Cufflinks does not produce XLOC and TCONS IDs. Cuffmerge produces them and Cuffdiff uses them. You should be able to use Cuff Ids if you want since they also carry chromosome location information.

[jolin0701-dy]

Thanks. But I do remember cufflinks also produce XLOC and TCONS IDs in the fpkm_tracking files. My question is how to connect CUFF IDs with XLOC or TCONS IDs. Since my interests are the linker RNA that can not be transcripted, but they do have Ensemble IDs.