Hi
I ran cuffcompare with the reference annotation "refGene.gtf" which is RefSeq Genes (refGene) track from UCSC GB.
I noticed that in the "*.combined.gtf" output there is an attribute oId instead of p_id:
When I ran cuffdiff, the "cds.diff" and "cds.fpkm_tracking" files came out empty:
Any suggestions will be appreciated.
Thanks
I ran cuffcompare with the reference annotation "refGene.gtf" which is RefSeq Genes (refGene) track from UCSC GB.
Code:
cuffcompare -V -r refGene.gtf -R -o s7_s8_refGene transcripts_s7.gtf transcripts_s8.gtf
Code:
chr1 Cufflinks exon 4797909 4798063 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00001337"; exon_number "1"; oId "s_8.310184.1"; nearest_ref "NM_008866"; class_code "j"; tss_id "TSS1"; chr1 Cufflinks exon 4798536 4798567 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00001337"; exon_number "2"; oId "s_8.310184.1"; nearest_ref "NM_008866"; class_code "j"; tss_id "TSS1";
Code:
cuffdiff -N -L s_7,s_8 -p 2 -v -r ~/mm9.fa s7_s8_refGene.combined.gtf accepted_hits_s7.bam accepted_hits_s8.bam .......... Processed 18302 loci. Performed 4816 isoform-level transcription difference tests Performed 574 tss-level transcription difference tests Performed 2853 gene-level transcription difference tests Performed 0 CDS-level transcription difference tests Performed 203 splicing tests Performed 131 promoter preference tests Performing 0 relative CDS output tests Writing isoform-level FPKM tracking Writing TSS group-level FPKM tracking Writing gene-level FPKM tracking Writing CDS-level FPKM tracking
Thanks
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