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Catch up
To avoid further issues with job submission, let's just copy alignment results to our $SCRATCH area.
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mkdir -p $SCRATCH/core_ngs/results
cd $SCRATCH/core_ngs/results
cp /corral-repl/utexas/BioITeam/core_ngs_tools/results/*.* . |
Overview and Objectives
Once raw sequence files are generated (in FASTQ format) and quality-checked, the next step in most NGS pipelines is mapping to a reference genome. For individual sequences of interest, it is common to use a tool like BLAST to identify genes or species of origin. However, a typical example NGS dataset may have tens to hundreds of millions of reads, which BLAST and similar tools are not designed to handle.
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