Question

I have a problem when I am using the bedGraphToBigWig.

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7.5 years ago

ghostforever.shi ▴ 50

When I use bedGraphToBigWig program to transform the bdg file generated from MACS2 to a bigwig file, I faced with a big problem as shown below. invalid unsigned integer: "html>"

did anyone know how to fix this problem? Much appreciate.

ChIP-Seq • 3.7k views

ADD COMMENT • link 7.5 years ago by ghostforever.shi ▴ 50

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what are the outputs of

file the_file_generated_by_macs2.bgd

and

head the_file_generated_by_macs2.bgd

?

ADD REPLY • link 7.5 years ago by Pierre Lindenbaum 164k

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the macs2 will generate bedGraph file in default mode, isn't it? That is the source of my bgd file

ADD REPLY • link 7.5 years ago by ghostforever.shi ▴ 50

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again, please, show us the outputs of the two command lines.

ADD REPLY • link 7.5 years ago by Pierre Lindenbaum 164k

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ChIP_calling_treat_pileup.bgd is the file I used for bedGraphToBigWig; BTW, I still don't quite understand your meaning, since I don't have any outputs but invalid unsigned integer: "html>".
Really apologize for this.

ADD REPLY • link 7.5 years ago by ghostforever.shi ▴ 50

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BTW, I still don't quite understand your meaning,

Run the commands exactly like @Pierre gave above and copy/paste what gets printed on screen here. Use your own file name instead of the_file_generated_by_macs2.bgd below.

file the_file_generated_by_macs2.bgd

ADD REPLY • link 7.5 years ago by GenoMax 147k

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OKOK,I got it, here is the outputs:

file ChIP_calling_treat_pileup.bdg

ChIP_calling_treat_pileup.bdg: ASCII text

head ChIP_calling_treat_pileup.bdg

chr19_gl000208_random   0   5898    0.00000
chr19_gl000208_random   5898    6102    1.00000
chr19_gl000208_random   6102    35080   0.00000
chr19_gl000208_random   35080   35092   1.00000
chr19_gl000208_random   35092   35131   2.00000
chr19_gl000208_random   35131   35284   3.00000
chr19_gl000208_random   35284   35296   2.00000
chr19_gl000208_random   35296   35320   1.00000
chr19_gl000208_random   35320   35334   2.00000
chr19_gl000208_random   35334   35335   3.00000

ADD REPLY • link updated 7.5 years ago by GenoMax 147k • written 7.5 years ago by ghostforever.shi ▴ 50

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ADD REPLY • link 7.5 years ago by GenoMax 147k

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It sounds like one of your input files is not what you expect (and that you accidentally downloaded an html file instead of a bed file)

ADD REPLY • link 7.5 years ago by Chris Miller 22k

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Oh, I got it, perhaps it could be the hg19.chrom.size file, since the bgd (bedGraph) file was generated by macs2 program, it won't be an html file actually. I will try it tomorrow. Hope it can solve the problem