Question: How to determine your reference fasta and gtf file match?
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gravatar for gkuffel22
3.2 years ago by
gkuffel22170
United States
gkuffel22170 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
cufflinks mirnaseq • 750 views
ADD COMMENTlink written 3.2 years ago by gkuffel22170
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