How to find out TSS and TTS from rice transcriptome data ?
Hello Researchers
How to find out TSS and TTS from rice transcriptome data ?
I have gtf file which contains only exons ?
Thank you
transcriptome
tss
tts
rice
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What is the source of your GTF? You can always filter
Oryzaout of Ensembl-plant (https://plants.ensembl.org/species.html) and obtain a full gff3 for the desired species.