Hi everyone
I assembled my RNA_seq data using tophat and cufflinks. But the assemble result seems strange. The length of exons were very short and most time, one transcript only contains one exon. I ran tophat and cufflinks using the default parameters, did I do something wrong? Here is some examples:
chr1 Cufflinks exon 1374518 1374621 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "901
.2568132303"; frac "1.000000"; conf_lo "0.000000"; conf_hi "2373.585808"; cov "0.389115";
chr1 Cufflinks transcript 2986172 2986198 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "6948.5151239
471"; frac "1.000000"; conf_lo "0.000000"; conf_hi "14971.969279"; cov "3.000000";
chr1 Cufflinks exon 2986172 2986198 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "694
8.5151239471"; frac "1.000000"; conf_lo "0.000000"; conf_hi "14971.969279"; cov "3.000000";
do you have some idea about that?
thanks
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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