sort command with large bed file (ENCODE-I)

greenelab / GCB535

Materials for GCB535 at Penn.

BSD 3-Clause "New" or "Revised" License

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sort command with large bed file (ENCODE-I) #179

Open bvoight opened 6 years ago

bvoight commented 6 years ago

with the reduced memory and options for exploration, some students pick up a gigantic .bed file, then run the usual sort -k1,1 -k2,2n command which subsequently dies.

I ended up writing a little script to help (sort_bed.pl) so next year I wonder if we distribute this helper script to them and modify the homework accordingly so that we can side-step this memory issue.

zhouzilu commented 5 years ago

Restrict file size for now. Push to 2020