Data Wrangling - Create Panopea-generosa-vv0.74.a4 Intron and Intergenic BED Files

Since generating an updated Pgenerosa_v074 annotation, we also needed updated intergenic and intron bed files to put in the OSF repository for this project.

I generated intergenic and intron BED files by following along with Steven’s notebooks:

Steven intergenic BED file notebook (GitHub):

• 30-Creating-intragenic-track.ipynb

Steven intron BED file notebook (GitHub):

• 24-Creating-intron-track.ipynb

Here’s how I generated these two BED files.

Jupyter Notebook (GitHub):

• 20191030_swoose_pgen_v074.a4_intron_intergenic_features.ipynb

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RESULTS

Output folder:

• 20191030_pgen_v074.a4_intron_intergenic_features/

Intergenic BED file (BED):

• Panopea-generosa-vv0.74.a4.intergenic.bed

Intron BED file (BED):

• Panopea-generosa-vv0.74.a4.introns.bed

Will add these files to the OSF repository for this project.

Here’s how they look in IGV:

IGV screencap showing intron and intergenic bed files