SIM2GTF is a simple method for performing SAM/BAM direct conversion to GTF format. While perhaps not exceptionally useful for short-read data, it might aid in investigations of long spliced RNA-seq reads such as those generated by the PacBio IsoSeq, CCS or Oxford Nanopore platforms. Reads can be directly converted into GTF bypassing assembly step, enabling direct comparison of observed transcript structures via other conventional methods such as gffread, gffcompare, ORFanage, etc.
$ git clone https://github.com/alevar/sam2gtf.git $ cd sam2gtf
Requirements Install the Rust compiler with rustup
- Install https://rustup.rs/.
- Test installation
$ rustup override set stable $ rustup update stable
Building
$ cargo build --release
$ sam2gtf -h