#Cufflinks# Can I change the tracking id?

Question

[hyeonjin]

Hi, all

I need to change tracking id about genes.fpkm_tracking and isoforms.fpkm_tracking. (cufflinks output)

for example,

I have

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
Xkr4 - - Xkr4 Xkr4 TSS27105 1:3214481-3671498 - - 0 0 0 OK
Rp1 - - Rp1 Rp1 TSS2867,TSS6138 1:4290845-4409241 - - 0 0 0 OK
Sox17 - - Sox17 Sox17 TSS26180 1:4490927-4497354 - - 0 0 0 OK
Lypla1 - - Lypla1 Lypla1 TSS27011 1:4807892-4846735 - - 18.4067 17.3559 19.4575 OK
Mrpl15 - - Mrpl15 Mrpl15 TSS25007 1:4773199-4785726 - - 29.7552 28.1379 31.3726 OK

(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
NM_001011874 - - Xkr4 Xkr4 TSS27105 1:3214481-3671498 3634 0 0 0 0 OK
NM_001195662 - - Rp1 Rp1 TSS6138 1:4290845-4409241 3047 0 0 0 0 OK
NM_011283 - - Rp1 Rp1 TSS2867 1:4343506-4360314 7508 0 0 0 0 OK
NM_001289467 - - Sox17 Sox17 TSS26180 1:4490927-4497354 2897 0 0 0 0 OK
NM_001289464 - - Sox17 Sox17 TSS26180 1:4490927-4497354 3288 0 0 0 0 OK

(isoforms.fpkm_tracking)

I want to convert tracking id to ensembl gene id in genes.fpkm_tracking.

and want to convert tacking id to ensembl transcript ID in isoforms.fpkm_tracking.

Do you have any cufflinks options? or Do you know any methods to convert them?

thank you.

[Jeffin Rockey]

It should be possible using appropriate gtf having gene_id Ensembl-Gene-Id;transcript_id Ensembl-Transcript-Id in the 9th column. i.e. Usually it is the value that comes in the above two fields that becomes the tracking id.

[cpad0112]

in short, gtf from ensembl.