backup.md

Backup files

If something happens and you are unable to create the files during a particular lesson, backup files we created are all found here on the image 'RNASeq_1DayWorkshop':

/opt/rnaseq/

Input raw fastq data

Download from OSF repository:

curl -L https://osf.io/365fg/download -o nema_subset_0Hour.zip
curl -L https://osf.io/9tf2g/download -o nema_subset_6Hour.zip
unzip nema_subset_0Hour.zip
unzip nema_subset_6Hour.zip

Trimmed reads

/opt/rnaseq/trim/*.qc.fq.gz

Transcriptome assembly

/opt/rnaseq/assembly/nema_trinity/Trinity.fasta

Annotation, created with this annotation lesson

/opt/rnaseq/annotation/Trinity.fasta.dammit/nema_gene_name_id.csv

Salmon quantification files

/opt/rnaseq/quant/*.quant