Input file

[LIUXING-bio]

Hi sir: What kind of input file should it be? Is it possible for mRNA_seq?

[olivertam]

Hi,

Thank you for your interest in the software. TEtranscripts uses BAM files as input, and it is designed for bulk RNA-seq (total or mRNA). It is not designed for single-cell or single-nuclei RNA seq. You will also need a gene annotation GTF (typically obtained from Refseq, GENCODE or Ensembl), and a TE GTF (which we have generated for many genome builds) Please let us know if this does not address your question.

Thanks

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[666lixiaona]

Hi,

For TE GTF (which we have generated for many [genome builds] your platform provide ,do they have the differences? Where can I search a BAM profile as a reference?

Thanks.

[olivertam]

Hi,

Could you clarify your question? Do you mean "What are the differences between the genome builds?"

Thanks.

[666lixiaona]

HI,

I want to know whether these profiles have the difference if I use them.

Thanks

[olivertam]

Hi,

If you are referring to the GTF from the same species (e.g. hg38, GRCh38_Ensembl and GRCh38_GENCODE), the difference is in the chromosome name for each of them. UCSC (hg38) has a chr in front of all their chromosome names (including scaffolds), while Ensembl (GRCh38_Ensembl) does not (e.g. chr1 in hg38 is 1 in GRCh38). Since our program (and most other genome interval tools) are trying to match chromosomes by their name, you need to use the TE GTF that has the corresponding chromosome name/ID. GENCODE is a mixed one, where canonical chromsomes has chr in front (e.g. chr1), but the scaffolds do not (and follow the Ensembl) nomenclature. Thus, if you're using GENCODE FASTA and gene GTF, you would need the GENCODE TE GTF for the quantification to work correctly.

Thanks.

[666lixiaona]

Thank you very much.