how I can add type=bedGraph to my bedgraph file?
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mikysyc2016
have trouble to upload data to washU browser
Hi, I want to use bigwig file to see my ChIP-seq results on WashU browser. I use sorted bedgraph as below to convert to bigwig. but when i upload bigwig washU show "Error at line 1: variableStep but not 2 fields" and i can see :
Showing first 10 rows from the total of 277168 rows: &��� X��`� 0�0�6� �� #9�9�3�ʓ��������0������� ���P�3Zh�ʏ�������01����� P��4���-x��t@����A��� B���xchr1��� chr10'��chr11�0Cchr12:>:chr13�d+chr14pRvchr15>5+chr16.;�chr17˾�chr18 ?ichr19 ��chr2 wA�
but my bedgraph is fine:
chr1 0 3000513 0.00000
chr1 100000164 100000253 1.00000
chr1 100000253 100000272 2.00000
chr1 100000272 100000276 3.00000
chr1 100000276 100000331 4.00000
chr1 100000331 100000389 3.00000
chr1 100000389 100000406 4.00000
chr1 100000406 100000420 5.00000
chr1 100000420 100000439 4.00000
chr1 100000439 100000443 3.00000
Can I get any suggestion? Thanks!
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jared.andrews07
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mikysyc2016
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mikysyc2016
1 answer
You need to put track type=bedGraph as the first line in your file, at a minimum. See the bedgraph format guidelines for other options, as stated in genomax's comment..
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jared.andrews07
Open it in a text editor, it's just a text file.
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Devon Ryan
Can i directly add type=bedgraph into the file without open it? The file is two big very hard to open. What kind command i can use ? Thanks,
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mikysyc2016
Make a text file with that line and then cat your_bedgraph >> that_file.
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Devon Ryan
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Please use the formatting bar (especially the
codeoption) to present your post better. I've done it for you this time.Thank you!
Check the format for bedgraph file here and then compare yours.
Thank you for your help.^^