Question: have trouble to upload data to washU browser
0
gravatar for mikysyc2016
3 months ago by
mikysyc201620
mikysyc201620 wrote:

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!

chip-seq sequence • 209 views
ADD COMMENTlink modified 3 months ago by jared.andrews071.3k • written 3 months ago by mikysyc201620

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

ADD REPLYlink written 3 months ago by genomax55k

Check the format for bedgraph file here and then compare yours.

ADD REPLYlink written 3 months ago by genomax55k

Thank you for your help.^^

ADD REPLYlink written 3 months ago by mikysyc201620
0
gravatar for jared.andrews07
3 months ago by
jared.andrews071.3k
St. Louis, MO
jared.andrews071.3k wrote:

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..

ADD COMMENTlink modified 3 months ago • written 3 months ago by jared.andrews071.3k

how I can add type=bedGraph to my bedgraph file?

ADD REPLYlink written 3 months ago by mikysyc201620
1

Open it in a text editor, it's just a text file.

ADD REPLYlink written 12 weeks ago by Devon Ryan84k

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,

ADD REPLYlink written 12 weeks ago by mikysyc201620
1

Make a text file with that line and then cat your_bedgraph >> that_file.

ADD REPLYlink written 12 weeks ago by Devon Ryan84k
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