...
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mkdir -p $SCRATCH/core_ngs/cutadapt
cd $SCRATCH/core_ngs/cutadapt
cp $CORENGS/human_stuff/Sample_H54_miRNA_L004_R1.cat.fastq.gz .
cp $CORENGS/human_stuff/Sample_H54_miRNA_L005_R1.cat.fastq.gz .
cp $CORENGS/yeast_stuff/Yeast_RNAseq_L002_R1.fastq.gz .
cp $CORENGS/yeast_stuff/Yeast_RNAseq_L002_R2.fastq.gz .
cp $CORENGS/tacc/cuta.cmds . |
Alignment workflow
Setup
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| Catchup_align_setup |
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| Catchup_align_setup |
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Alignment workflow setupStarting files:
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# FASTA (for building references)
mkdir -p $SCRATCH/core_ngs/references/fasta
cp $CORENGS/references/*.* $SCRATCH/core_ngs/references/fasta/
# FASTQ (to align)
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/*fastq.gz $SCRATCH/core_ngs/alignment/fastq/
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| Catchup_references |
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| Catchup_references |
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ReferencesGet a copy of references we build in the exercises (including FASTA):
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mkdir -p $SCRATCH/core_ngs/references
rsync -ptlvrP $CORENGS/references/ $SCRATCH/core_ngs/references/
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