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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Combine genes named by MSTRG in different sample with prepDE.py #209

Open tenger-github opened 5 years ago

tenger-github commented 5 years ago

Dear Pertea, As you mentioned, MSTRG gene tags are unique in one sample. However, MSTRG tags are not uniform between samples and should not be used as a way to identify genes across samples.

  1. How does prepDE.py combine the same gene in different samples? by genomic location or attributes like ref_gene_id ?
  2. After extraction of gene count with prepDE.py, there are also genes named with MSTRG tag. where are these MSTRG tags from? New assignment by prepDE.py? OR from Stringtie-derived GTF files?
  3. In gene count file produced by prepDE.py, there are only gene ID and reads counts. However, for MSTRG tagged genes, how to know these genes information such as genomic location?

I greatly appreciate your reply.

Sincerely Yours.