[BioC] [Genome] "Error Unrecognized format line 1..." when using "Add Custom Tracks"

[Peng Yu]

Hi Galt,

I am not sure how to add the track information to the .bw file.

Shall I use the following command?

cat track_info_file old.bw > new.bw

Regards,
Peng

On Tue, Aug 4, 2009 at 8:23 PM, Galt Barber<galt at sundance.cse.ucsc.edu> wrote:
>
> please see step 7 of
>  http://genome.ucsc.edu/goldenPath/help/bigWig.html
>
> You need to do this:
>
> at the add custom track form, type in the track name etc.,
> and supply the parameter dataUrl pointing to your
> binary bigwig test.bw, i.e.
>
> track type=bigwig name="someName" {other params go here}
>  dataUrl=http://chalk.brc.bcm.edu/wl1/pengy/test.bw
>
> This track line is a single line, and it can be long.
>
> (sometimes special characters in the dataUrl value may requre
> url-encoding)
>
> -Galt
>
>
> On Tue, 4 Aug 2009, Peng Yu wrote:
>
>> Hi Jennifer,
>
> Please see my .wig file and the script to generate the .bw file below.
>
> Then, I went to http://genome.ucsc.edu/cgi-bin/hgGateway and click
> 'add custom track". In "genome" selection box, I chose "mouse". And I
> chose "July 2007" assembly.
>
> I input the following address in the box under "Paste URLs or data:"
>
> http://chalk.brc.bcm.edu/wl1/pengy/test.bw
>
> Then, I click "submit". It gives me the following error message.
>
>    Error Unrecognized format line 1 of
> http://chalk.brc.bcm.edu/wl1/pengy/test.bw: &ü ˆ  (note: chrom names
> are case sensitive)
>
> Would you please follow the procedure and see what the problem is?
>
> Regards,
> Peng
>
> $ cat test.wig
> variableStep chrom=chr10 span=10
> 3001501 1
> 3001511 1
> 3001521 1
> 3001531 1
> 3001541 1
> 3001551 1
> 3001561 1
> 3001571 1
>
> $ cat run.sh
> #!/usr/bin/env bash
> fetchChromSizes mm9 > mm9.chrom.sizes
> wigToBigWig test.wig mm9.chrom.sizes test.bw
>
>
> On Tue, Aug 4, 2009 at 11:59 AM, Jennifer Jackson<jen at soe.ucsc.edu> wrote:
>>
>> Hello, It appears that your track definition lines is not formatted
>> correctly Please see the instructions at this help page, specifically item
>> #7: http://genome.ucsc.edu/goldenPath/help/bigWig.html Try the adjustment
>> and please let us know if you continue to have problems Thank you, Jen
>>
>> ps. Attachments are not posted to the mailing list, so pasting some
>> example data into an email was an excellent idea. In the future, you can
>> also mention that you have example to share in file format. We can make
>> arrangements to obtain the file(s) off the list.
>>
>> ------------------------------------------------
>> Jennifer Jackson
>> UCSC Genome Bioinformatics Group
>>
>> ----- "Peng Yu" <pengyu.ut at gmail.com> wrote:
>>
>>> From: "Peng Yu" <pengyu.ut at gmail.com>
>>> To: genome at soe.ucsc.edu
>>> Sent: Tuesday, August 4, 2009 8:32:33 AM GMT -08:00 US/Canada Pacific
>>> Subject: Re: [Genome] "Error Unrecognized format line 1..." when using
>>> "Add Custom Tracks"
>>>
>>> On Mon, Aug 3, 2009 at 8:13 PM, Peng Yu<pengyu.ut at gmail.com> wrote:
>>> > Hi,
>>> >
>>> > I want to add the attached file in the following webpage.
>>> >
>>> > http://genome.ucsc.edu/cgi-bin/hgCustom
>>> >
>>> > However, it shows the following webpage. I don't understand what the
>>> > problem is. Can somebody help me?
>>> >
>>> > Error Unrecognized format line 1 of <some web
>>> > link>/NA_MACS_no_track_small.bw: &ü ˆ  (note: chrom names are case
>>> > sensitive)
>>>
>>> I send the above message with an attachment. But somehow, it is not
>>> posted in the mailing list archive.
>>>
>>> NA_MACS_no_track_small.bw was generated in the following commands. I
>>> tried to add the track. But I got the above error message. Can
>>> somebody let me know what I was wrong?
>>>
>>> $ fetchChromSizes mm9 > mm9.chrom.sizes
>>> $ wigToBigWig NA_MACS_no_track_small.wig mm9.chrom.sizes
>>> NA_MACS_no_track_small.bw
>>> $ cat NA_MACS_no_track_small.wig
>>> variableStep chrom=chr10 span=10
>>> 3001501 1
>>> 3001511 1
>>> 3001521 1
>>> 3001531 1
>>> 3001541 1
>>> 3001551 1
>>> 3001561 1
>>> 3001571 1
>>>
>>> BTW, does this mailing list accept emails with attachments?
>>>
>>> Regards,
>>> Peng
>>>
>>> _______________________________________________
>>> Genome maillist  -  Genome at soe.ucsc.edu
>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome