Hi Katrina,
Please ignore my message below i sent you few minutes before
re: conservation score for mm9. It was my mistake and it's a irrelevant
question. Mouse has 19 chromosomes and all of them are there. Please
ignore my previous email and do not post it online.
thanks & regards
Bibek
Bibek wrote:
> Hi Katrina,
> Please ignore my message below i sent you few minutes
> before. It was my mistake. Mouse has 19 chromosomes and all of them
> are there. Please ignore my previous email and do not post it online.
>
> thanks & regards
> Bibek
>
> Bibek wrote:
>> Hi Katrina,
>> Thank you for your reply.
>> I tried to download mouse mm9 phastcons score through FTP from
>> hgdownload.cse.ucsc.edu/goldenPath/mm9/phastCons30way/vertebrate.
>> After download is complete, I realized that conservation score data
>> files for chromosome 20, 21 & 22 are not available. I have following
>> questions-
>>
>> (1) Why conservation scores for 3 chromosome, i.e. 20, 21 & 22 are
>> not available at ftp server for mm9. Does it mean these 3 chromosomes
>> are not conserved at all. Where can i get scores for these 3
>> chromosomes?
>>
>> (2) Is there any threshold value for conservation score based on
>> which we can define a particular block of gene to be ideally
>> conserved. For example, some people have used 0.57 as conservation
>> score threshold for mammalian microRNA targets.
>>
>> Hope to hear from you soon.
>>
>> Thanking you.
>> Bibek
>>
>> Katrina Learned wrote:
>>> Hi Bibek,
>>>
>>> I must correct part of my answer below:
>>>
>>> One of our engineers let me know that talking about the 'mean' of
>>> phastCons or phyloP is misleading. He says, "These are not numbers
>>> that can be combined like that. There is a log odds score in the
>>> 'Most Conserved' regions that is an accurate summary of these
>>> numbers." There are some discussions about this mathematical problem
>>> by Adam Siepel in the mail list. This discussion indicates the
>>> complication of trying to use these numbers in normal statistical
>>> calculations:
>>> https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008744.html
>>> and follow up information:
>>> https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008748.html
>>>
>>> For more information about the 'Most Conserved" track referred to by
>>> our engineer, see the track description here:
>>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=mostConserved30way.
>>>
>>> Thank you,
>>>
>>> Katrina Learned
>>> UCSC Genome Bioinformatics Group
>>>
>>>
>>> Katrina Learned wrote, On 11/05/10 10:04:
>>>> Hi Bibek,
>>>>
>>>> For information about step (and PhastCons files in general), see
>>>> http://genome.ucsc.edu/goldenPath/help/phastCons.html. Also, on
>>>> that page is this information about gaps, "A new declaration line
>>>> is inserted in the file when the /chrom/ value changes, when a gap
>>>> is encountered (requiring a new /start/ value), or when the /step/
>>>> interval changes." There are a many reasons why there are gaps, one
>>>> being that where there is no conservation, there is no score (this
>>>> is the nature of the HMM models that are making these numbers).
>>>>
>>>> For calculating the conservation score for a small region, you can
>>>> use the mean. See this previously answered question for more
>>>> information:
>>>> https://lists.soe.ucsc.edu/pipermail/genome/2009-July/019616.html
>>>>
>>>> For your last question, the easiest way to do this is using our
>>>> Table Browser tool. Click on "Tables" on the blue bar on the top of
>>>> the main page. In the Table Browser, select mm9 as well as the
>>>> track and table you are using (Conservation; phastCons30way), and
>>>> then create an intersection with the genes track of your choice
>>>> (click "create" next to "intersection:"). For more information
>>>> about using the Table Browser see "Using the Table Browser" by
>>>> scrolling down past the Table Browser form or the "User's Guide"
>>>> at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. For
>>>> specific information about creating intersections, see
>>>> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection.
>>>>
>>>> Please don't hesitate to contact the mail list again if you have
>>>> any further questions.
>>>>
>>>> Katrina Learned
>>>> UCSC Genome Bioinformatics Group
>>>>
>>>> Bibek wrote, On 11/05/10 07:01:
>>>>
>>>>> Hi,
>>>>> I downloaded phastcons score of mouse (mm9) through FTP
>>>>> (hgdownload.cse.ucsc.edu) from
>>>>> /goldenPath/mm9/phastCons30way/vertebrate. I checked file,
>>>>> chr1.data & found that first block starts at 3000306, whereas next
>>>>> block starts at 3002512. See below-
>>>>> fixedStep chrom=chr1 start=3000306 step=1
>>>>> fixedStep chrom=chr1 start=3002512 step=1
>>>>>
>>>>> I believe each line on this file represents each position of
>>>>> chromosome, being step=1. Please clarify if i am wrong.
>>>>>
>>>>> The difference between beginning of above 2 blocks is 2207, but i
>>>>> found only 2175 lines for phastcons score. This indicate that
>>>>> phastcons scores of few bases (about 32) are not given in the
>>>>> file. Does it mean 32 nucleotides before start of next block (i.e.
>>>>> 3002512) do not show alignment & thus no score. Please clarify.
>>>>>
>>>>> Another query, If i wish to calculate conservation score of a
>>>>> stretch of 7-8 nucleotides, what should i adopt.
>>>>>
>>>>> Lastly, if i wish to convert chromosomal coordinates of these
>>>>> files into positions within the gene, which method or track file
>>>>> of mm9 should i use.
>>>>>
>>>>> Thank you in advance.
>>>>>
>>>>> regards,
>>>>> Bibek
>>>>>
>>>>>
>>>>>
>>>>>
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>>>>>
>>>>>
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>>>>>
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>>
>
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