I'm confused...

You ask us to download over a megabyte of data in a gzipped tar file that contains two files:

Code:

NA12878_newheader_base_counts_lessthan_30reads_perbase.bed
NS12911_newheader_base_counts_lessthan_30reads_perbase.bed

Neither of which are referenced by the above above code (even after removing the parenthetical elements from the file list).
And, if we change the script above to:

Code:

awk '{A[$3] += $2} END{for (i in A) print i, A[i]}' NA12878_newheader_base_counts_lessthan_30reads_perbase.bed NS12911_newheader_base_counts_lessthan_30reads_perbase.bed > all_genes_bases.txt

the output produced is never going to have anything with an alphabetic string in the 1st output field because neither of these input file contain any alphabetic characters in their third fields.

Please explain what is going on here!