cufflinks : difference in --GTF and --GTF-guide result

[masterpiece]

Hi all,


I've run transcriptome data analysis on bacteria samples. However, I'm puzzle on expression result differences between --GTF and --GTF-guide option used when run cufflinks. All parameters that I've used to run both sets are the except for cufflinks, one with --GTF and the other --GTF-guide. Here is the "isoforms.fpkm_tracking" from both run

cufflinks with --GTF option

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
PL0001.t01 - - - - NC_006350 0-1116 1116 54.9354 90.6693 83.0938 98.2448 OK
PL0002.t01 - - - - NC_006350 1160-2375 1215 39.0997 65.3895 59.2786 71.5004 OK
PL0003.t01 - - - - NC_006350 3113-5096 1983 8.92195 15.1043 12.8893 17.3193 OK
PL0005.t01 - - - - NC_006350 5868-7209 1341 33.7041 56.7591 51.3899 62.1284 OK
PL0006.t01 - - - - NC_006350 7527-8013 486 260.334 428.281 398.744 457.818 OK
PL0010.t01 - - - - NC_006350 13451-13862 411 53.5034 88.5618 72.9061 104.217 OK
PL0009.t01 - - - - NC_006350 12162-13380 1218 27.5019 46.1215 40.9969 51.2461 OK
PL0011.t01 - - - - NC_006350 14009-14462 453 181.027 309.998 283.268 336.728 OK
PL0012.t01 - - - - NC_006350 14616-15096 480 73.6868 122.777 106.793 138.762 OK

cufflinks with --GTF-guide option

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
PL0001.t01 - - - - NC_006350 0-1116 1116 0 0 0 0 OK
PL0002.t01 - - - - NC_006350 1160-2375 1215 0 0 0 0 OK
PL0003.t01 - - - - NC_006350 3113-5096 1983 0 0 0 0 OK
PL0005.t01 - - - - NC_006350 5868-7209 1341 0 0 0 0 OK
PL0006.t01 - - - - NC_006350 7527-8013 486 0 0 0 0 OK
PL0007.t01 - - - CUFF.160 NC_006350 8394-10668 2274 0 0 0 0 LOWDATA
PL0008.t01 - - - CUFF.160 NC_006350 10664-12158 1494 0 0 0 0 LOWDATA
PL0009.t01 - - - CUFF.160 NC_006350 12162-13380 1218 0 0 0 0 LOWDATA
PL0010.t01 - - - - NC_006350 13451-13862 411 0 0 0 0 OK
PL0011.t01 - - - CUFF.160 NC_006350 14009-14462 453 0 0 0 0 LOWDATA

And why some of the genes have FPKM of "0" but at the same time it gives FPKM_status as "OK"?


- kamal