Links to Scripts

HTStream

slurm script for preprocessing using slurm task array and htstream

hts_preproc.slurm

hts_preproc_SE.slurm

hts_preproc_TagSeq.slurm

shell script for preprocessing using bash loop and htstream.

hts_preproc.sh

hts_preproc_SE.sh

hts_preproc_TagSeq.sh

R script to produce summary table, assumes exact htstream operations and order as described above.

summary_stats.R

summary_stats_SE.R

summary_stats_TagSeq.R

Star alignment

slurm script for indexing the genome

star_index.slurm

shell script for indexing the genome

star_index.sh

slurm script for mapping using slurm task array and star

star.slurm

star_SE.slurm

shell script for mapping using bash loop and star.

star.sh

star_SE.sh

shell script to produce summary mapping table

star_stats.sh

Salmon alignment

slurm script for indexing the genome

salmon_index.slurm

shell script for indexing the genome

salmon_index.sh

slurm script for mapping using slurm task array and star

salmon.slurm

shell script for mapping using bash loop and star.

salmon.sh

R script to produce summary mapping table

salmon_stats.R

Matt’s R scripts from final day

Matt’s final Rmd file for DE_analysis.Rmd

Matt_DE_Analysis.Rmd

Matt’s final Rmd file for enrichment.Rmd

Matt_enrichment.Rmd