Question: Average PhastCon score using bedops
gravatar for Shaway
4.2 years ago by
Shaway10 wrote:

I want to uss bedops to some peaks' average phastCon score, and I followed this Average PhastCon score for a bed file

But when I use sort-bed to sort my bedfile, it report an error "Non-numeric end coordinate", I don't know what's bed file is as follows(no header, just chr1).

chr1 846692 846703

chr1 873947 873958

chr1 873947 873958

chr1 902385 902396

if I using starch non-sorted file(starch chr1_AP1_peak.bed > chr1_ap_s.starch), it report ERROR: BED data is missing chromosome and/or coordinate data ERROR: BED data could not be transformed. ERROR: Could not write transformed/compressed data to output file pointer.

I don't konw how to deal with it. can any body help me,thanks!

starch bedops software error • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 4.2 years ago by Shaway10

If you'd still like help with this, please post the results of running:

$ head chr1_AP1_peak.bed | cat -te -

This will suggest if there are problems with the formatting of your input file, which could trip up other tools.

ADD REPLYlink written 4.1 years ago by Alex Reynolds31k
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