Question: WUSTL gateway compatible bed format
1
gravatar for Wet&DryImmunology
4.4 years ago by
Japan
Wet&DryImmunology220 wrote:

I ran into a bed file format term called : "WUSTL gateway compatible bed" I tried to search the term with Google, but got no obvious hits.

Does anyone know what that kind of bed file looks like? Thanks!

I came across with this term when I tried to read code of ROSE algorithm developed by Richard Young's group: https://bitbucket.org/young_computation/rose ( I tried to use the ROSE to analyze my own data, but had some issues: https://bitbucket.org/young_computation/rose/issues/26/unexpected-running-result-using-rose)

in the Python file ROSE_utils.py, they format bed file as follows:

def formatBed(bed,output=''):

'''
formats a bed file from UCSC or MACS into a WUSTL gateway compatible bed
'''
newBed = []

if type(bed) == str:
    bed = parseTable(bed,'\t')

indexTicker = 1
for line in bed:

    newLine = line[0:4]
    try:
        strand = line[5]
    except IndexError:
        strand = '.'
    newLine+= [indexTicker,strand]
    indexTicker +=1
    newBed.append(newLine)

if len(output) > 0:
    unParseTable(newBed,output,'\t')
else:
    return newBed

it seems to me that they added a fifth column column with " ." as value to the normal bed file generated from MACS to format the "WUSTL gateway compatible bed", is that correct? I wonder the fact that they used different format of bed file might be the cause of my issue.

Update: I could successfully apply ROSE to my other data "cooked" following exactly the same pipeline , so it seems the formatBed function has nothing to do with my previous issues. Also, after careful reading of the whole code, it seems to me actually the formatBed function were never called. so I will leave the question here for pure curiosity reasons.

chip-seq sequence next-gen • 1.2k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Wet&DryImmunology220
2

I'm at WUSTL and have never heard of that format, for what it's worth. Can you edit your question and paste a few lines from the head of the file?

ADD REPLYlink written 4.4 years ago by Chris Miller21k

Hi, Chris. Sorry that I did not explain it very well, please see the edited question.

ADD REPLYlink written 4.4 years ago by Wet&DryImmunology220

What a weird format. The first 4 columns of a BED6 file, plus the line number then the strand (or . if it's not there). If that's what it needs then certainly inputting a regular BED file will break things.

ADD REPLYlink written 4.4 years ago by Devon Ryan96k
2

Yes, I don't know who cooked up that format, but it certainly wasn't my group! :)

ADD REPLYlink written 4.4 years ago by Chris Miller21k
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