Error of intersection of BED datasets

Question: Error of intersection of BED datasets

3.4 years ago by

Russian Federation

Hello! As a result of intersection of BED files the empty file is created. Example of source files: File 1: http://pastebin.com/qrrrMvE2 File 2: http://pastebin.com/KN58nHD4

software error bed intersection galaxy intersect • 1.0k views

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modified 3.3 years ago • written 3.4 years ago by platon.work • 0

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

These BED files are not really in BED format. The coordinates in each describe a range of "0" bases.

Example of one:

track name="chr6 32721547 rs9275765 BED" description=""
chr6    32715344        32715344
chr6    32715605        32715605
chr6    32715986        32715986

Note that the start (column 2) and stop (column 2) are the same value. I am not sure where this was obtained, but for the first data line, this could be:

chr6    32715343        32715344  ==> would designate base "32715344"

BED file specification is here: https://wiki.galaxyproject.org/Learn/Datatypes#Bed

Also, before using many tools that work with BED (or Interval) datasets, it is a good idea to first remove the track (and browser) lines if present. Tools in Text Manipulation can help with removing lines (Remove first lines of a dataset), adjusting data values (Compute), and cutting out columns to reconstruct the proper format (Cut).

Thanks! Jen, Galaxy team

ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

I am not sure where this was obtained

These are SNPs obtained by HaploReg v3.

Another example (with nonzero delta and without titles):

Dataset-1:

chr6 32372459 32372461

chr6 32407918 32407920

chr6 32408399 32408401

Dataset-2:

chr6 32372459 32372461

chr6 32407918 32407920

chr6 32408399 32408401

chr6 32460285 32460287

chr6 32460302 32460304

chr6 32460338 32460340

The empty file is as a result of intersection created

ADD REPLY • link modified 3.4 years ago • written 3.4 years ago by platon.work • 0

3.3 years ago by

platon.work • 0

Russian Federation

platon.work • 0 wrote:

Please reply to my last comment. Thanks in advance!

ADD COMMENT • link written 3.3 years ago by platon.work • 0

Hello,

First, Double check the datatype and column assignment on the inputs. Click on the pencil icon for the datasets to review this metadata and adjust it as needed. The type should be "bed" or "interval" and the columns labeled as Chrom (1), Start (2), and End (3).

If there are still problems, please share the exact tool you are using, the settings, and where the job is being run (http://usegalaxy.org or elsewhere?). If this was not at http://usegalaxy.org, please try to see if the problem can be replicated there as additional troubleshooting - we may ask for a shared history.

Thanks! Jen, Galaxy team

ADD REPLY • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

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