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YY-TMU / InPACT

A computational method designed to identify and quantify IPA sites via the examination of contextual sequence patterns and RNA-seq reads alignment.
MIT License
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How to deal with gencode gtf file #8

Open sunqiangzai opened 3 months ago

sunqiangzai commented 3 months ago

How to deal with gencode gtf file

liuxc1995 commented 3 months ago

InPACT is designed to work with annotations from RefSeq, and currently, the GENCODE GTF file format is not compatible with InPACT.

sunqiangzai commented 2 months ago

Thank you, another question is [Salmon](https://github.com/COMBINE-lab/salmon) is used to index and quantify the transcriptome, and then the usage is calculated. which fasta file is used to generate salmon index?

liuxc1995 commented 2 months ago

The FASTA file is generated from merged.gtf produced from "InPACT_transcript". Tools like gffread can be used to extract the transcript sequences from the GTF file and generate the required FASTA file.