Hi, Joseph!
Your example is in BED 5 form.
Genome Graphs (GG) only accepts
its own GG input formats, of which bed
is not among them.
You can read all the details
at the links that Jen sent earlier in this thread.
Typically it looks like
chrom position value
or
marker value
---
GG can also support multiple values on a single line.
In which case each additional column is treated as
a value in the next set.
So the bed 5 is being mistakenly interpreted as
chrom position value1 value2 value3
--
To convert your data into something GG can use,
one possible approach might be to
keep the first column, average col 2 and 3,
keep the last column:
chr1 44006 44066 region_0 564
becomes
chr1 44036 564
A simple awk script to do this might be
cat oldBed5File | awk '{print $1 " " ($2+$3) " " $5} > newGgFile
Then you can either paste that new file's contents into the
input form, or you can upload it from a local file,
or you can stick it on your web space somewhere
and just paste in the URL.
-Galt
Ar 7/27/2010 4:34 PM, scríobh Joseph Kingston:
> Greetings again,
>
> I am trying to upload data into the Genome Graphs tool using BED file format
> and
> I still can't get it to work. Even the example data provided in the FAQ will
> not
> upload. It doesn't show any error message at all. It says it uploaded
> completely
> but --nothing-- appears in the drop down list. This is a sample of the data I
> am
> trying to upload, is there anything wrong with it?
>
> track name=pairedReads description="Clone Paired Reads" useScore=1
> chr1 44006 44066 region_0 564
> chr1 46023 46083 region_1 672
> chr1 47390 47601 region_2 760
> chr1 48251 48311 region_3 31
> chr1 80315 80375 region_4 171
> chr1 83080 83140 region_5 18
> chr1 84485 84545 region_6 200
>
>
> Joseph
>
>
> ----- Forwarded Message ----
> From: Jennifer Jackson<[email protected]>
> To: Joseph Kingston<[email protected]>
> Cc: [email protected]
> Sent: Mon, July 26, 2010 7:11:03 PM
> Subject: Re: [Genome] Zebrafish Graph
>
> Hello Joseph,
>
> The Genome Graph's function requires specific input formats. The format
> that you are loading is not in this set (BED4).
>
> This help page linked off the Genome Graph's home page can help:
> http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html
>
> Specifically, see the sections about Formatting Data and the Examples.
>
> Please feel free to contact the mailing list support team again if you
> would like more assistance.
>
> Warm regards,
>
> Jen
> UCSC Genome Browser Support
>
> On 7/26/10 5:19 PM, Joseph Kingston wrote:
>> Hello,
>>
>> I am a first time user of Genome Graphs. I am trying to upload my own data
> into
>> Genome Graphs but it seems to have no effect. The options I choose are as
>> follows:
>> Clade: Vertebrate
>> genome: Zebrafish
>> assembly: Zv8
>>
>> Then I click upload and paste in the data included below (leaving all other
>> fields unchanged). I submit the form to get the following "Data Upload
>> Complete"
>> message. However, on the 'graph' drop-down list my upload is not shown. It is
>> just a list with --nothing-- in it. Is there something wrong with the data I
> am
>> uploading?
>>
>> Data Upload Complete (1559 bytes)
>>
>>
>>
>> These data are now available in the drop-down menus on the main page for
>> graphing.
>>
>> Thank you for your help,
>> Joseph
>>
>> ________________________________
>> browser position chr1:44006-44066
>> track name="input_immatureT"
>> #Chromosome StartPosition EndPosition RegionName Score
>> chr1 44006 44066 region_0 564
>> chr1 46023 46083 region_1 672
>> chr1 47390 47601 region_2 760
>> chr1 48251 48311 region_3 -31
>> chr1 80315 80375 region_4 -171
>> chr1 83080 83140 region_5 -18
>> chr1 84485 84545 region_6 200
>> chr1 164425 164485 region_7 557
>> chr1 165078 165138 region_8 887
>> chr1 174603 174663 region_9 401
>> chr1 201776 201836 region_10 -592
>> chr1 205894 205954 region_11 234
>> chr1 206899 206959 region_12 -95
>> chr1 269936 270155 region_13 841
>> chr1 272603 272663 region_14 450
>> chr1 273072 273132 region_15 804
>> chr1 274649 274709 region_16 135
>> chr1 303976 304036 region_17 33
>> chr1 495304 495364 region_18 91
>> chr1 502144 502204 region_19 445
>> chr1 503071 503131 region_20 390
>> chr1 562783 563017 region_21 790
>> chr1 581465 581755 region_22 -168
>> chr1 673678 673738 region_23 -159
>> chr1 676089 676149 region_24 148
>> chr1 1463640 1463700 region_25 31
>> chr1 2055855 2055915 region_26 648
>> chr1 2056770 2056830 region_27 529
>> chr1 2058602 2058662 region_28 -55
>> chr1 2238513 2238573 region_29 259
>> chr1 2447697 2447757 region_30 908
>> chr1 2451604 2451664 region_31 -184
>> chr1 2509550 2509824 region_32 638
>> chr1 2512283 2512343 region_33 178
>> chr1 2559324 2559384 region_34 272
>> chr1 2561162 2561222 region_35 -2
>> chr1 2561726 2562576 region_36 -162
>> chr1 2562954 2563014 region_37 -70
>> chr1 2564525 2564585 region_38 122
>> chr1 2564868 2564928 region_39 87
>> chr1 2566578 2566638 region_40 -82
>> chr1 2566962 2567022 region_41 327
>>
>>
>>
>>
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
>
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
