Page Comparison

# 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

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

Overview

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1. Convert text-format SAM files into binary BAM files (samtools view -b) and vice versa (just samtools view)
2. Sort BAM files by reference coordinates (samtools sort)
3. Index BAM files that have been sorted (samtools index)
4. Filter alignment records based on BAM flags, mapping quality or location (samtools view)

Since Ad we've seen, since BAM files are binary, they can't be viewed directly using standard Unix file viewers such as more, less and head. We have seen how, butsamtools view can be used to convert binary-format BAM files into text format for viewing. But samtools view also has options that let you do powerful filtering of the output. We focus on this filtering capability in this set of exercises.

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idev -m 180 -N 1 -A OTH21164 -r CoreNGS-Fri     # or -A TRA23004
# or
idev -m 90 -N 1 -A OTH21164 -p development  # or -A TRA23004

Next set up a directory for these exercises, and copy an indexed BAM file there. This is the yeast_pe.sort.bam file from our The Basic Alignment Workflow exercises.

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