/gannet/Atumefaciens/20190625_stringtie_oly_v081/

Transcript isoform identification/annotation of the MAKER-annotated Olurida_v081 genome using Hisat2 and Stringtie.

Used trimmed (Trimmomatic) RNAseq FastQs from my 20180827 Trinity transcriptome assembly.

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FILES

- .gtf: Individual GTF files produced by Stringtie.

- .cov_refs.gtf: Individual coverage files produced by Stringtie.

- *_hisat2.err: Individual Hisat2 alignment stats.

- *.sorted.bam: Individual sorted BAM files.

- *.sorted.bam.bai: Individual BAM index files.

- 20190625_stringtie_oly_v081.sh: SBATCh script for running on Mox.

- fastq.list.txt: List of input FastQ files for Stringtie.

- gtf_list.txt: List of individual GTF files. Used for Stringtie merge command.

- Olurida_v081.stringtie.gtf: Merged GTF file.

- slurm-999805.out: Mox SLURM output (i.e. stderr/stdout).

- system_path.log: List of Sam's Mox system $PATH contents.

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Notebook:

https://robertslab.github.io/sams-notebook/2019/06/25/Genome-Annotation-O.lurida-(v081)-Transcript-Isoform-ID-with-Stringtie-on-Mox.html