GTF input file

[dvirdi01]

It says that SUPPA takes in fastq files and also genome annotation GTF file. By genome annotation does it mean the reference genome gtf file? I assembled my long reads using stringtie and it also gives its output in the gtf format. I wasn't sure if I am suppose to give it the assembled transcriptome output gtf file from Stringtie or the reference genome file?

Also, I tried running suppa generateEvents -f ioe and ioi for my Stringtie output which was an assembled transcriptome file of all the input files I gave it. Suppa generated the ioe and ioi files but I am not sure whether it produced the right output. Would Suppa work correctly on an assembled transcriptome gtf file?

[EduEyras]

Hi,

you can use a GTF generated by yourself with e.g. StringTie or any other method.

The important thing is that the GTF contains transcripts and genes, and that you have at least the "exon" lines (tab separated):

chr14 Ensembl exon 73741918 73744001 0.0 - . column9

where column9 is of the form (single space separated):

gene_id "gene_ID"; transcript_id "transcript_ID";

where gene_ID may contain several transcript_ID values

If stringtie or any other program does not give you genes and transcripts, you can run SUPPA with the --pool-genes option, which will create the genes and transcripts for you:

see https://github.com/comprna/SUPPA#command-and-options

I hope this helps

best

Eduardo

On Fri, 20 Oct 2023 at 05:28, dvirdi01 @.***> wrote:

It says that SUPPA takes in fastq files and also genome annotation GTF file. By genome annotation does it mean the reference genome gtf file? I assembled my transcriptome using stringtie and it also gives its output in the gtf format. I wasn't sure if I am suppose to give it the assembled transcriptome or the rewference genome file?

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