Content Comparison

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idev -m 120 -N 1 -A OTH21164 -r core-ngs-class-0606

# or, without a reservation
idev -m 120 -N 1 -A OTH21164 -p development 

module load biocontainers
module load bedtools
bedtools --version   # should be bedtools v2.27.1

...

idev -m 120 -N 1 -A OTH21164 -r core-ngs-class-0606

# or, without a reservation:
idev -m 120 -N 1 -A OTH21164 -p development 

module load biocontainers
module load bedtools
bedtools --version   # should be bedtools v2.27.1

...

idev -m 120 -N 1 -A OTH21164 -r core-ngs-class-0606

# or, without a reservation
idev -m 120 -N 1 -A OTH21164 -p development 

module load biocontainers
module load bedtools
bedtools --version   # should be bedtools v2.27.1

...

idev -m 120 -N 1 -A OTH21164 -r core-ngs-class-0606

# or, without a reservation:
idev -m 120 -N 1 -A OTH21164 -p development

module load biocontainers
module load samtools
module load bedtools

mkdir -p $SCRATCH/core_ngs/bedtools_multicov
cd $SCRATCH/core_ngs/bedtools_multicov
cp $CORENGS/catchup/bedtools_merge/merged*bed .
cp $CORENGS/yeast_rnaseq/yeast_mrna.sort.filt.bam* .

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• Go to the UCSC Genome Browser: https://genome.ucsc.edu/
• Select Genomes from the top menu bar
• Select Human from POPULAR SPECIES
  • under Human Assembly select Feb 2009 (GrCh37/hg19)
  • select GO
• In the hg19 browser page,
  • the 100 Vert. Cons track is a signal track
    • the x-axis is the genome position
    • the y-axis represents the base-wise conservation among vertebrates
  • customize the 100 Vert. Cons track
    • right-click on "100 Vert. Cons" text in the left margin,
      • select "Configure 100 Vert. Cons" from the menu
    • in the 100 Vert. Cons Track Settings dialog:
      • change "Track height" to 100
      • change "Data view scaling" to "auto-scale to data view"
      • click "OK"
  • the Layered H3K27Ac track is a signal track
    • the x-axis is the genome position
    • the y-axis represents the count of ChIP-seq reads that overlap each position
      • where the ChIP'd protein is H3K27AC (histone H3, acetylated on the Lysine at amino acid position 27)

The bedtools genomecov function (https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html), with the -bg (bedgraph) option produces output in bedGraph format. Here we'll analyze the per-base coverage of yeast RNAseq reads in our merged yeast gene regions.

...

idev -m 120 -N 1 -A OTH21164 -r core-ngs-class-0606

# or, without a reservation:
idev -m 120 -N 1 -A OTH21164 -p development 

module load biocontainers
module load bedtools
bedtools --version   # should be bedtools v2.27.1

...