Question: Converting MSTRG from stringtie with gene name
gravatar for fhassanz
2.6 years ago by
fhassanz20 wrote:


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

rna-seq stringtie • 6.6k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.6 years ago by fhassanz20

I couldn't fix the problem. Thank you!

ADD REPLYlink written 2.6 years ago by fhassanz20
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