I am confused cufflinks results：
1. the cuffcompare result to reference GTF show some cufflinks assembled transcripts "=" (classcode) reference genes, these genes with a "=" transcripts will be predicted correctly, BUT there are many other classcode (c,i,j..), it illustrate these genes may predicted wrong. One of my purpose is find the genes wrong predicted, how can find this from the cufflinks or cuffcompare results? Should I choose a FPKM threshould?
2. Some transcripts in cufflinks have a same gene ID, Is these genes are alternative splicing? if not, how should I get the alternative splice from cufflinks results?
1. the cuffcompare result to reference GTF show some cufflinks assembled transcripts "=" (classcode) reference genes, these genes with a "=" transcripts will be predicted correctly, BUT there are many other classcode (c,i,j..), it illustrate these genes may predicted wrong. One of my purpose is find the genes wrong predicted, how can find this from the cufflinks or cuffcompare results? Should I choose a FPKM threshould?
2. Some transcripts in cufflinks have a same gene ID, Is these genes are alternative splicing? if not, how should I get the alternative splice from cufflinks results?
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