Dear, When use cufflinks, I encounter a big problem. If use “cufflinks –G”, it not assemble any novel genes and isoforms. But “cufflinks –g” also encounter problem. The result shows as follow:
55 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "2"; FP
56 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "3"; FP
57 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "4"; FP
58 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "5"; FP
59 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "6"; FP
60 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "7"; FP
61 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "8"; FP
62 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "9"; FP
63 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "10"; F
64 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "11"; F
65 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "12"; F
66 309 - . gene_id "CUFF.2"; transcript_id "NM_015155"; exon_number "13"; F
I want know why it recognize the “transcript_id”, while doesn’t know “gene_id”.
A big problem is that the cuffdiff output is also confusion. It show as follow:
『gene_exp.diff』
1509 XLOC_001508 XLOC_001508 RERE chr1:8492712-8493573 q1 q2 OK
1510 XLOC_001509 XLOC_001509 RERE chr1:8494713-8494999 q1 q2 OK
1511 XLOC_001510 XLOC_001510 RERE chr1:8503067-8503472 q1 q2 OK
1512 XLOC_001511 XLOC_001511 RERE chr1:8505909-8506863 q1 q2 OK
1513 XLOC_001512 XLOC_001512 RERE chr1:8506981-8508284 q1 q2 OK
1514 XLOC_001513 XLOC_001513 RERE chr1:8515100-8515631 q1 q2 OK
1515 XLOC_001514 XLOC_001514 RERE chr1:8530511-8531476 q1 q2 OK
1516 XLOC_001515 XLOC_001515 RERE chr1:8531644-8532531 q1 q2 OK
1517 XLOC_001516 XLOC_001516 RERE chr1:8539576-8540626 q1 q2 OK
1518 XLOC_001517 XLOC_001517 RERE chr1:8555242-8555810 q1 q2 OK
1519 XLOC_001518 XLOC_001518 RERE chr1:8564935-8565810 q1 q2 OK
1520 XLOC_001519 XLOC_001519 RERE chr1:8567281-8567763 q1 q2 OK
1521 XLOC_001520 XLOC_001520 RERE chr1:8571715-8572103 q1 q2 OK
1522 XLOC_001521 XLOC_001521 RERE chr1:8588952-8589191 q1 q2 OK
1523 XLOC_001522 XLOC_001522 RERE chr1:8589400-8589863 q1 q2 OK
1524 XLOC_001523 XLOC_001523 RERE chr1:8589926-8590744 q1 q2 OK
1525 XLOC_001524 XLOC_001524 RERE chr1:8599237-8600354 q1 q2 OK
1526 XLOC_001525 XLOC_001525 RERE chr1:8605236-8605710 q1 q2 OK
1527 XLOC_001526 XLOC_001526 RERE chr1:8605782-8605992 q1 q2 OK
It is the gene_exp.diff (not isoform_exp.diff), the same gene is separated to so many lines. I also used cufflinks in Galaxy and get the same results. I don’t find a solution, so I seek help from your, thanks.
