Gene IDs after updated prepDE.py

[asumann]

Hi,

I am having trouble with geneIDs in gene_count_matrix file. I will give an example:

This transcript MSTRG.43175 found twice in the matrix. And they do not have the same expression as can be seen below.

SRR7185486 SRR7185487 SRR7185505 SRR7185506 SRR7185508 SRR7185510 SRR7185511 SRR7185517 SRR7185518 SRR7185537 SRR7185553
MSTRG.43175               0          0        128          0          0          0          0          0          0          0          0
MSTRG.43175|RXRB          0          0          2        140          0          0          0         12          0          0          0

I checked merged GTF file(mstrg_43175.txt). It has many MSTRG.43175 transcripts as expected. I do not see any problem in that.

Could you help me understand the discrepancy I see in the gene_count_matrix file?

Happy New Year! Asuman

[asumann]

Any update? @gpertea