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Tip

title	Reservations

Use our summer school reservation (CoreNGS

-Thu

) when submitting batch jobs to get higher priority on the ls6 normal queue

today:sbatch --reservation=CoreNGS-Thu <batch_file>.slurm

.

Code Block

language	bash
title	Request an interactive (idev) node

# Request a 180 minute interactive node on the normal queue using our reservation
idev -m 120 -N 1 -A OTH21164 -r CoreNGS
idev -m 120 -N 1 -A TRA23004 -r CoreNGS

# Request a 120 minute idev node on the development queue 
idev -m 120 -N 1 -A OTH21164 -p development
idev -m 120 -N 1 -A TRA23004 -p development

Code Block

language	bash
title	Submit a batch job

# Using our reservation
sbatch --reseservation=CoreNGS <batch_file>.slurm

Note that the reservation name (CoreNGS) is different from the TACC allocation/project for this class, which is OTH21164.

Table of Contents

Exercise #3: PE alignment with BioITeam scripts

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In this exercise, we will use some RNA-seq data from Vibrio cholerae, published on GEO here, and align it to a reference genome.

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Exercise #3: PE alignment with BioITeam scripts