Creating a gtf annotation file from a FASTA (& bam?) for non-model organism
I performed de novo transcriptome assembly. Have the FASTA file that I am using as my reference and also performed alignments of my reads back to that. I have been using stringtie to create gtf files for the differential expression analysis (counting requires a gtf file) but I am trying to do this at gene level. Stringtie creates its own IDs for alternative splicing/isoforms. I do not want this. I can't see a way around this so is there a way I can create a gtf annotation file based on my fasta file I use for my reference?
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Try SuperTranscripts (can be constructed by Lace or utility in Trinity).
![enter image description here][1]So I ran supertranscripts (which I am using that FASTA file from it) but the gtf file it gave with it, gave really really odd entries. Here is a snapshot of it:
https://ibb.co/NC9HF89
First, let's fix the picture: How to add images to a Biostars :-)
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or this....