Using the ce4 browser, nucleosome track, "sense" subtrack,
the description says the following:
---
Display Conventions and Configuration
In each of the sub-tracks, sequences starting at the same base pair were
collapsed and color-coded from the lightest to the darkest color in five
shades according to the following category-based scale:
Number of read instances Color shade
1 lightest
2 light
3-5 medium
6-10 dark
more than 10 darkest
Hold your mouse over individual items in each track to see the number of
read instances starting at that base pair.
---
It appears that score is the number of reads.
You are correct.
-Galt
[email protected] wrote:
> Hi,
>
> I'm loking at the data I downloaded from you, and I'm not quite sure that
> I understand the meaning of the columns.
>
> the data I downloaded are these: rsync -avz --progress
> rsync://hgdownload.cse.ucsc.edu/goldenPath/ce4/database/nucleosomeFragmentsSense.txt.gz
> which come from Valouev et al. Genome Res. 18(7), 1051-1063 (2008)
>
> I used describe table to figure out what the columns mean, they tell you
> this:
>
> mysql> describe nucleosomeFragmentsSense;
> +-------------+----------------------+------+-----+---------+-------+
> | Field | Type | Null | Key | Default | Extra |
> +-------------+----------------------+------+-----+---------+-------+
> | bin | smallint(5) unsigned | NO | | 0 | |
> | chrom | varchar(255) | NO | MUL | | |
> | chromStart | int(10) unsigned | NO | | 0 | |
> | chromEnd | int(10) unsigned | NO | | 0 | |
> | name | varchar(255) | NO | | | |
> | score | int(10) unsigned | NO | | 0 | |
> | strand | char(1) | NO | | | |
> | thickStart | int(10) unsigned | NO | | 0 | |
> | thickEnd | int(10) unsigned | NO | | 0 | |
> | reserved | int(10) unsigned | NO | | 0 | |
> | blockCount | int(10) unsigned | NO | | 0 | |
> | blockSizes | longblob | NO | | | |
> | chromStarts | longblob | NO | | | |
> +-------------+----------------------+------+-----+---------+-------+
>
> I've interpreted the 'score' column as the number of reads at the given
> position. is this correct?
>
> Thanks very much for your help,
> George Locke
>
>> Good point! I forgot to add db in my example too.
>>
>> -Galt
>>
>>
>> On Fri, 28 Aug 2009, Michael Pheasant wrote:
>>
>>> Try specifying the database you want for example:
>> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A hg18
>>
>> Dont know what database you want though; hg19, mm9, etc
>>
>> M
>>
>> On Fri, Aug 28, 2009 at 7:19 AM, GEORGE LOCKE<[email protected]>
>> wrote:
>>> Hi,
>>>
>>> I'm a grad student at Rutgers trying to get access to data from the
>>> genome
>>> browser mysql database. Â I'm doing research in nucleosome positioning
>>> with
>>> Prof. Alex Morozov.
>>>
>>> i logged on as suggested, mysql --user=genome
>>> --host=genome-mysql.cse.ucsc.edu -A
>>>
>>> this is the query I wish to execute:
>>> select chrom, chromStart, chromEnd, score, strand from
>>> nucleosomeFragmentsSense into outfile "dump.txt";
>>> (using database ce4)
>>>
>>> this is the error i get: ERROR 1045 (28000): Access denied for user
>>> 'genome'@'%' (using password: NO)
>>>
>>> what can I do? Â I can't find this information in text format anywhere
>>> and
>>> hoped I could just get it direct from the database but have been
>>> rebuffed.
>>>
>>> Regards,
>>> George
>>>
>>> _______________________________________________
>>> Genome maillist  -  [email protected]
>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>>
>>
>>
>> --
>> Michael Pheasant
>> Associate Project Scientist
>> UCSC Genome Browser
>>
>> Email: [email protected]
>> Skype: mpheasant
>> Phone: +1-831-459-1424
>>
>> Location: Engineering2 Room 515
>> Post: CBSE, UC Santa Cruz, MS:CBSE/ITI
>> 1156 High Street
>> Santa Cruz, CA 95064, USA
>>
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
