Hello, I used New Tuxedo protocol in which StringTie is used for quantification step using:
stringtie -e -B -p 8 -G merged_gtf -o SRRXXX.gtf SRRXXX.bam
gives the output files as following:
e2t.ctab e_data.ctab i2t.ctab i_data.ctab SRRXXX.gtf t_data.ctab
t_data.ctab columns are used for making countdata for DESeq2 using command
I tried to import t_data.ctab for DESeq2 with the help of tximport manual
tx2gene <- tmp[, c("t_name", "gene_name")]
but my t_data.ctab contains '.' in 'gene_name' column, which is inappropriate for creation of countdata. Therefore I can't proceed my differential expression of genes. My question is Can I use 'gene_id' column instead of 'gene_name' from t_data.ctab. Or am I supposed to directly switch the quantification tool itself, if yes then which tool will be better as compared to StringTie?