Question: I have a problem when I am using the bedGraphToBigWig.
0
gravatar for ghostforever.shi
3 months ago by
ghostforever.shi10 wrote:

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 • 243 views
ADD COMMENTlink written 3 months ago by ghostforever.shi10

what are the outputs of

file the_file_generated_by_macs2.bgd

and

head the_file_generated_by_macs2.bgd

?

ADD REPLYlink written 3 months ago by Pierre Lindenbaum98k

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

ADD REPLYlink written 3 months ago by ghostforever.shi10
1

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

ADD REPLYlink written 3 months ago by Pierre Lindenbaum98k

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 REPLYlink written 3 months ago by ghostforever.shi10

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 REPLYlink modified 3 months ago • written 3 months ago by genomax33k

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 REPLYlink modified 3 months ago by genomax33k • written 3 months ago by ghostforever.shi10
1

I have formatted your code correctly. In future use the icon shown below (after highlighting the text you want to format as code) when editing.

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ADD REPLYlink written 3 months ago by genomax33k

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 REPLYlink written 3 months ago by Chris Miller18k

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

ADD REPLYlink written 3 months ago by ghostforever.shi10

Thanks!I solve the problem!!! Much appreciate!

ADD REPLYlink written 3 months ago by ghostforever.shi10
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