Content Comparison

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The BED format

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idev -m 120 -N 1 -A OTH21164 -r CoreNGSday5 
# ...CoreNGS-Fri
# or
idev -m 90 -N 1 -A OTH21164 -p development

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

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• Most BEDTools functions now accept either BAM or BED files as input. 
  • BED format files must be BED3+, or BED6+ if strand-specific operations are requested.
• When comparing against a set of regions, those regions are usually supplied in either BED or GTF/GFF.
• All text-format input files (BED, GTF/GFF, VCF) should use Unix line endings (linefeed only).

The most important thing to remember about comparing regions using BEDTools, is that all input files must share the same set of contig names and be based on the same reference! For example, if an alignment was performed against a human GRCh38 reference genome from Gencode, use annotations from the corresponding GFF/GTF annotations.

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idev -m 120 -N 1 -A OTH21164 -r CoreNGSday5CoreNGS-Fri
# ... or
idev -m 90 -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 CoreNGSday5 CoreNGS-Fri
# or
idev -m 90 -N 1 -A OTH21164 -p development

Copy over the yeast RNA-seq files we'll need (also copy the GFF gene annotation file if you didn't make one).

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