i just do some practice on ballgown and stringtie , and i got some GTF file and ballgown`s file. however, i just find i cant use R or something else to deliver a excel file which contain FPKM. i think the excel file i want maybe looks like this :
gene_id FPKM A 124 B 541 C 122
please help me ,thanks a lot :)
Can you paste a few sample lines from the GTF file you are working with?
this is the top ten lines:
1 StringTie transcript 337772 338047 1000 + . gene_id "Zm00001d027250"; transcript_id "Zm00001d027250_T001"; cov "66.076088"; FPKM "8.407302"; TPM "14.141658"; 1 StringTie exon 337772 338047 1000 + . gene_id "Zm00001d027250"; transcript_id "Zm00001d027250_T001"; exon_number "1"; cov "66.076088"; 1 StringTie transcript 426764 432130 1000 + . gene_id "Zm00001d027254"; transcript_id "Zm00001d027254_T001"; cov "2.043083"; FPKM "0.259955"; TPM "0.437262"; 1 StringTie exon 426764 426798 1000 + . gene_id "Zm00001d027254"; transcript_id "Zm00001d027254_T001"; exon_number "1"; cov "0.000000"; 1 StringTie exon 426869 426970 1000 + . gene_id "Zm00001d027254"; transcript_id "Zm00001d027254_T001"
i think maybe a python script can extract the fpkm , but i dont know how to edit a complex python script.so i want to find some software to do this work.thanks a lot