I just do some practice on ballgown and stringtie, and I got some GTF file and ballgown`s file.

However, I just find I can't 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 :)

Form StringTie output you can use 'sample1_**gene_abund.tab**' file to extract these information,

**FPKM:**

    cat {sample1}_gene_abund.tab | cut -d$'\t' -f1,8 | sed "s/FPKM/sample1_FPKM/" | sed 's/Gene ID/gene_id/' > {sample1}_gene_abund.fpkm.txt


**TPM:**

    cat {sample1}_gene_abund.tab | cut -d$'\t' -f1,9 | sed "s/TPM/sample1_TPM/" | sed 's/Gene ID/gene_id/' > {sample1}_gene_abund.tpm.txt