Hello again, Preeti,
After taking a closer look at your attached PSL file, I think I see the
problem.
The 14th field is for "target sequence name" -- it is expecting a chrom name
in the form of "chr1" for example.
Additionally, I think the program is confused by the "name" in the 10th field
--
I'm not sure it's able to parse the pipes ("|").
match mis- rep. N's Q gap Q gap T gap T gap strand Q
Q Q Q T
T T T block blockSizes qStarts tStarts
match match count bases count bases name
size start end
name size start end count
---------------------------------------------------------------------------------------------------------------------------------------------------------------
27 0 0 0 0 0 0 0 +
simulated_der5_p2|1|:1:61124719-61124746 27 0 27 1
247249719 61125138 61125165 1 27, 0,
61125138,
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Ann Zweig wrote:
> Hello Preeti,
>
> Please see this online help doc for an explanation of how to use PSL
> files as Custom Tracks:
> http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL
>
> I hope this information is helpful to you. Please don't hesitate to
> contact the mail list again if you require further assistance.
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
>
> Sankaranarayanan Preethi wrote:
>>
>> Hi Hiram,
>>
>> Thank you for responding. But when I tried to run it
>> through the table browzer, i get the following error.
>>
>> Error File 'ref1.psl.txt' - Error line 6 of custom track: 1
>> not a recognized sequence (note: sequence names are case
>> sensitive)
>> I have also attached the file with just one line on it.
>> Could you please help?
>>
>> Thanks,
>> Preeti
>>
>>> --- On Sat, 14/11/09, Hiram Clawson <[email protected]>
>>> wrote:
>>>
>>>> From: Hiram Clawson <[email protected]>
>>>> Subject: Re: [Genome] psltobed.c
>>>> To: "Sankaranarayanan Preethi" <[email protected]>
>>>> Cc: [email protected]
>>>> Date: Saturday, 14 November, 2009, 12:04 PM
>>>> Good Evening Preethi:
>>>>
>>>> This is a program in the kent source tree.
>>>> http://genome.ucsc.edu/admin/cvs.html
>>>> http://genome.ucsc.edu/admin/jk-install.html
>>>>
>>>> It would be easier to enter your psl file as a custom
>>>> track into the genome browser, then use the table
>>>> browser to dump it back to you as a bed file.
>>>> http://genome.ucsc.edu/goldenPath/help/customTrack.html
>>>> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
>>>>
>>>> --Hiram
>>>>
>>>>
>>>> Sankaranarayanan Preethi wrote:
>>>>> Hi,
>>>>>
>>>>> I have no idea where should I download this file
>>> and
>>>> run. My problem is I have a .psl file. I need to
>>> convert it
>>>> to a .bed file. that is all. Could you please help me
>>> how to
>>>> do this? I tried checking on the genome browser
>>> webpage.
>>>> there is no download... I am confused. please help!
>>>>> Thanks,
>>>>> Preeti
>>>>>
>>>>>
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