Question: How to determine your reference fasta and gtf file match?
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gkuffel22 • 170 wrote:
I know I have asked this question before and the solution seems simple but I really do not understand how to tell if my reference fasta file and gtf file are compatible so that when I run Cufflinks gene id's will be populated with actual gene names. If I get a reference fasta (i.e. hg19) and a gtf file from iGenomes and ftp these to my local instance of Galaxy shouldn't they be a match? I have included some of my Cufflinks output so everyone can visualize the problem.
| 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 | - | - | chr10:862254-862277 | - | - | 131104 | 62780.3 | 199428 | OK |
| CUFF.2 | - | - | CUFF.2 | - | - | chr10:3152122-3152135 | - | - | 2.04138e+07 | 1.85674e+07 | 2.22601e+07 | OK |
| CUFF.3 | - | - | CUFF.3 | - | - | chr10:3822634-3822700 | - | - | 5350.73 | 1895.83 | 8805.63 | OK |
| CUFF.4 | - | - | CUFF.4 | - | - | chr10:5895653-5895746 | - | - | 2157.21 | 856.362 | 3458.05 | OK |
| CUFF.5 | - | - | CUFF.5 | - | - | chr10:16821449-16821461 | - | - | 1.98815e+07 | 1.78418e+07 | 2.19213e+07 | OK |
| CUFF.6 | - | - | CUFF.6 | - | - | chr10:21770697-21770747 | - | - | 112625 | 89770.6 | 135480 | OK |
| CUFF.7 | - | - | CUFF.7 | - | - | chr10:22518400-22518513 | - | - | 6322.11 | 4651.79 | 7992.44 | OK |
| CUFF.8 | - | - | CUFF.8 | - | - | chr10:26422592-26422615 | - | - | 139844 | 69922.1 | 209766 | OK |
| CUFF.9 | - | - | CUFF.9 | - | - | chr10:31840032-31840056 | - | - | 133015 | 68493.5 | 197537 | OK |