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| Code Block |
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| language | bash |
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| title | Look at GFF annotation entries with less |
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|
mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnaseq/sacCer3.R64-1-1_20110208.gff .
cp $CORENGS/yeast_rnarnaseq/yeast_mrna.sort.filt.bam* .
# Use the less pager to look at multiple lines
less sacCer3.R64-1-1_20110208.gff
# Look at just the most-important Tab-separated columns
cat sacCer3.R64-1-1_20110208.gff | grep -v '#' | cut -f 1,3-5 | head -20
# Include the ugly 9th column where attributes are stored
cat sacCer3.R64-1-1_20110208.gff | grep -v '#' | cut -f 1,3,9 | head |
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| Code Block |
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| mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnarnaseq/*.gff . |
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| Code Block |
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| language | bash |
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| title | Convert GFF to BED with BioITeam script |
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|
/work/projects/BioITeam/common/script/gtf_to_bed.pl sc_genes.gff 1 \
> sc_genes.converted.bed |
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| Code Block |
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| mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnarnaseq/*.gff .
cp $CORENGS/yeast_rnarnaseq/sc_genes* . |
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Exercise: How many genes in our sc_genes.bed file are in each category?
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| Code Block |
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| language | bash |
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| title | Setup for BEDTools exercises |
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|
# To catch up...
mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnarnaseq/sc_genes.bed* .
cp $CORENGS/yeast_rnarnaseq/*.gff .
# Copy the BAM file
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnarnaseq/yeast_mrna.sort.filt.bam* . |
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| Code Block |
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| idev -m 120 -N 1 -A OTH21164 -r CoreNGSday5
module load biocontainers
module load samtools
module load bedtools
mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnarnaseq/*.gff .
cp $CORENGS/yeast_rnarnaseq/sc_genes.bed* .
cp $CORENGS/yeast_rnarnaseq/yeast_mrna.sort.filt.bam* . |
|
...
| Expand |
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|
| Code Block |
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| mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rnarnaseq/*.gff .
cp $CORENGS/yeast_rnarnaseq/sc_genes.bed* .
cp $CORENGS/yeast_rnarnaseq/yeast_mrna.sort.filt.bam* .
module load biocontainers
module load bedtools |
|
...