/gannet/Atumefaciens/20190716_hisat2-build_20190709-olur_v081/

Generate a Hisat2 genome index that identifies splice sites and exons for downstream use with Stringtie to identify transcript isoforms in the MAKER-annotated 20190709-Olurida_v081 genome.

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FILES

- 20190709-Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gtf: GTF file created from GFF file of the same name. Created with GFF utilities.

- 20190716_hisat2-build_20190709-olur_v081.sh: SBATCh script for running on Mox.

- fastq.list.txt: List of input FastQ files for Stringtie. Not relevant to this analysis and can be ignored.

- hisat2_build.err: Standard error output.

- hisat2_exons.tab: Hisat2 exons text file. tab-delimited.

- hisat2_splice_sites.tab: Hisat2 splice sites text file. tab-delimited.

- *.ht2: Hisat2 index files.

- slurm-1049941.out: Mox output file (stderr/stdout).

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

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Notebook:

https://robertslab.github.io/sams-notebook/2019/07/16/Genome-Annotation-O.lurida-20190709-v081-Hisat2-Transcript-Isoform-Index.html