How to convert a .tsv annotation file to .gtf?

Question

[Ashley]

I am a first-time poster so I hope I am doing this okay.

I am trying to execute a genome indexing script. The following are my parameters:

--runThreadN 14 \
--runMode genomeGenerate \
--genomeDir /scratch/projects/ag_transcriptomics/transcriptomes \
--genomeFastaFiles /scratch/projects/ag_transcriptomics/transcriptomes/PSTR.fna \
--sjdbGTFfile /scratch/projects/ag_transcriptomics/transcriptomes/INDEX/WHEREMYFILEWOULDBE \
--sjdbOverhang 100 \
--sjdbGTFtagExonParentTranscript Parent

Unfortunately, the database I am accessing only has .tsv annotation files, not .gtf. I need a .gtf to create the index so that I can move on to the alignment step.

So, my question is, is there any way that I can make this .tsv into a .gtf that I can use? For reference, the .tsv is from the following database: http://comparative.reefgenomics.org/datasets.html

Thank you!

Answer 1

[GenoMax]

Unfortunately those "annotation" files appear to be blast search results. There is no information about chromosomal intervals of where the queries are from. If you did have that information available someplace else this would be a major task to convert this information into a GTF file.

If you have the transcriptome available then consider using salmon (LINK) instead of STAR.

[Ashley]

Okay thank you ! I will try that out.