Hi,
When I quantifies expression levels for the features of the transcriptome using StringTie, some results in the output really made me confused.
In the e_data.ctab
,the coverage of a transcripts is really high and actually many reads mapped to the reference genome at this site.
e_id chr strand start end rcount ucount mrcount cov cov_sd mcov mcov_sd
23 scaffold_1 + 87462 87575 64 64 64.00 43.7895 11.0743 43.7807 11.0660
24 scaffold_1 + 87674 88356 253 249 251.00 47.9561 12.6755 47.5183 12.7022
But in the t_data.ctab
and the GTF file, the results are different
scaffold_1 StringTie transcript 87462 88356 1000 + . gene_id "estExt_fgenesh1_pg.C_10011"; transcript_id "127031"; cov "0.920524"; FPKM "3.685930"; TPM "15.617980";
scaffold_1 StringTie exon 87462 87575 1000 + . gene_id "estExt_fgenesh1_pg.C_10011"; transcript_id "127031"; exon_number "1"; cov "0.000000";
scaffold_1 StringTie exon 87674 88356 1000 + . gene_id "estExt_fgenesh1_pg.C_10011"; transcript_id "127031"; exon_number "2"; cov "1.074169";
the coverage and FPKM are very low, I don't know why. Do anyone have ideas