I used Stringtie V1.3.3b to estimate transcript abundances and create table counts for Ballgown. This was the command: stringtie -e -B -p 8 -G stringtie_merged.gtf -o ballgown/ATRX-315Lacz1/ATRX-315Lacz1.hisat.gtf ATRX-315Lacz1.hisat.bam
Ballgown output for genes that show statistically signifcant differences between groups does not contain the genes' names. Instead they are labeled with MSTRG.X. Here is a small part of my result:
feature id fc pval qval
gene MSTRG.21995 8.403143715 0.01540734 0.709610488
gene MSTRG.12086 6.418374935 0.275564702 0.751109325
gene MSTRG.15181 6.315061048 0.069660273 0.709610488
I couldn't find any thing already discussed this problem. Could you please help me to fix the problem. I need to get the gene's name from Ballgown, instead of the MSTRG tag. Or is there any way to convert them top gene names?
Thank you very much for your help. I really appreciate it. Farshad