I have been looking for answers in different forums and then thought let me write here in the hope of an answer to my simple question, which may have been answered before:
I am using HISAT2 GrCh38 release 84 version for the genome as provided by the developers and then using Ensembl GTF version 113 (latest in 2024) for annotating the genes in Stringtie "prep.DE.py" script to get gene expression levels across samples. The index was built using Ensembl v84, which is outdated. Is it okay to proceed like this? The output has a lot of genes which do have high expression but no gene name since they are novel.
Hi StringTie team,
I have been looking for answers in different forums and then thought let me write here in the hope of an answer to my simple question, which may have been answered before:
I am using HISAT2 GrCh38 release 84 version for the genome as provided by the developers and then using Ensembl GTF version 113 (latest in 2024) for annotating the genes in Stringtie "prep.DE.py" script to get gene expression levels across samples. The index was built using Ensembl v84, which is outdated. Is it okay to proceed like this? The output has a lot of genes which do have high expression but no gene name since they are novel.
Thank you!