Hi,
I am facing an issue with getting cufflinks results with Arabidopsis. The problem seems to be the reference gtf.
When I ran cufflinks without a reference gtf, I got FPKM values for genes in the genes.fpkm_tracking file.
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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 - - Chr1:3675-3911 - - 49.5395 33.4668 65.6123 OK
CUFF.2 - - CUFF.2 - - Chr1:3995-4272 - - 30.6876 20.7312 40.6439 OK
CUFF.3 - - CUFF.3 - - Chr1:4467-5098 - - 21.4671 17.3165 25.6177 OK
----------------------------------------------
But when I ran cufflinks with a reference gtf.
I am not getting any FPKM values.
----------------------------------------------
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
XLOC_000001 - - XLOC_000001 ANAC001 TSS1 1:3630-5899 - - 0 0 0 OK
XLOC_003797 - - XLOC_003797 ARV1 TSS3983 1:5927-8737 - - 0 0 0 OK
XLOC_003798 - - XLOC_003798 NGA3 TSS3984 1:11648-13714 - - 0 0 0 OK
----------------------------------------------
I am aware that cufflinks/cufffdiff need a compatible reference genome format. So for both these cufflinks runs I used a compatible reference.gtf file, which was created as follows:
I also ran cufflinks using the ncbi genes.gtf (instead of using the cuffcmp.combined.gtf), but I still got no FPKM calculations in the result file.
I also ran cuffdiff with the cuffcmp.combined.gtf, and here again I did not get any FPKM values, and hence, I am getting a NOTEST.
Would grealty appreciate your help in figuring out what is the problem.
Thanks in advance,
Ash
I am facing an issue with getting cufflinks results with Arabidopsis. The problem seems to be the reference gtf.
When I ran cufflinks without a reference gtf, I got FPKM values for genes in the genes.fpkm_tracking file.
----------------------------------------------
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 - - Chr1:3675-3911 - - 49.5395 33.4668 65.6123 OK
CUFF.2 - - CUFF.2 - - Chr1:3995-4272 - - 30.6876 20.7312 40.6439 OK
CUFF.3 - - CUFF.3 - - Chr1:4467-5098 - - 21.4671 17.3165 25.6177 OK
----------------------------------------------
But when I ran cufflinks with a reference gtf.
I am not getting any FPKM values.
----------------------------------------------
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
XLOC_000001 - - XLOC_000001 ANAC001 TSS1 1:3630-5899 - - 0 0 0 OK
XLOC_003797 - - XLOC_003797 ARV1 TSS3983 1:5927-8737 - - 0 0 0 OK
XLOC_003798 - - XLOC_003798 NGA3 TSS3984 1:11648-13714 - - 0 0 0 OK
----------------------------------------------
I am aware that cufflinks/cufffdiff need a compatible reference genome format. So for both these cufflinks runs I used a compatible reference.gtf file, which was created as follows:
- Downloaded NCBI dataset for Arabidopsis from http://cufflinks.cbcb.umd.edu/igenomes.html
- took genes.gtf file
- created cuffcombined.gtf using this command: cuffcompare -s /ccmb/CoreBA/BioinfCore/Common/DATA/Cufflinks_Data/Arabidopsis/Arabidopsis_thaliana/NCBI/build9.1/Sequence/WholeGenomeFasta/genome.fa -CG -r ../arabidopsis_genes.gtf ../arabidopsis_genes.gtf
- Used cuffcmp.combined.gtf which was created as the reference.gtf
I also ran cufflinks using the ncbi genes.gtf (instead of using the cuffcmp.combined.gtf), but I still got no FPKM calculations in the result file.
I also ran cuffdiff with the cuffcmp.combined.gtf, and here again I did not get any FPKM values, and hence, I am getting a NOTEST.
Would grealty appreciate your help in figuring out what is the problem.
Thanks in advance,
Ash
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