[Bioc-sig-seq] Minimal short sequences position/orientation container

[Ivan Gregoretti]

Hi Patrick,

Great. It works.

Can you clarify if the following observation is a feature or a bug?

When I download

http://dl.getdropbox.com/u/2051155/myTags.bed

and from the unix prompt I take a peek at it, I get:

head myTags.bed

chr1	3002444	3002479			+
chr1	3002989	3003024			-
chr1	3017603	3017638			+
chr1	3017879	3017914			-
chr1	3018173	3018208			+
chr1	3018183	3018218			-
chr1	3018183	3018218			-
chr1	3019065	3019100			+
chr1	3019761	3019796			-
chr1	3020044	3020079			-

fine. It shows the 36 bases long reads.

Now I follow your suggestion loading it into R:

suppressMessages(library(rtracklayer))

myTags <- import('myTags.bed')

ranges(myTags["chr1"])[[1]]
IRanges instance:
             start       end width
[1]        3002445   3002479    35
[2]        3002990   3003024    35
[3]        3017604   3017638    35
[4]        3017880   3017914    35
[5]        3018174   3018208    35
[6]        3018184   3018218    35
[7]        3018184   3018218    35
[8]        3019066   3019100    35
[9]        3019762   3019796    35
...            ...       ...   ...
[322808] 197166880 197166914    35
[322809] 197167672 197167706    35
[322810] 197167851 197167885    35
[322811] 197185820 197185854    35
[322812] 197185850 197185884    35
[322813] 197188518 197188552    35
[322814] 197189251 197189285    35
[322815] 197189593 197189627    35
[322816] 197191697 197191731    35

So, all start positions are shown as starting one nucleotide upstream
from the original record and the features are reported as being 35
bases long instead of 36.

Is it feature or bug?

Thank you

Ivan


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878



On Thu, Sep 24, 2009 at 2:51 AM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
> Ivan,
> The RangedData class can store strand information in its values table. The
> values table can store any "vector-like" object from simple R vectors
> (including lists) to an instance of any of the *List classes defined in
> IRanges. If you use rtracklayer's import function on a bed file containing
> the information you have shown, the chromosome information will be used to
> segment the other values into spaces, the start and end values will be
> joined together in the ranges information (as a CompressedIRangesList
> object) and the strand information will be stored as a factor column across
> the values set (which is a CompressedDataFrameList object). The strand
> information can be accessed by the strand accessor function. If your data
> are sorted by strand within chromosome, you could add another level of
> compression by storing the strand information as a 'factor' Rle in the
> values table instead of a plain factor. rtracklayer's export function is
> aware of a possible strand column in the values table and handles it
> appropriately when serializing a RangedData object back into a bed file.
>
>
> Patrick
>
>
> Ivan Gregoretti wrote:
>>
>> Hi everybody,
>>
>> What is the minimal container class for position-and-orientation of
>> Solexa reads?
>>
>>
>> For example, the minimal positional information should be something
>> like a BED record, like this
>>
>> chr1\t3000001\t3000036\t\t\t+\t
>> ...(and many more lines)...
>>
>> sorry for the cumbersome string but I just want to stress that the
>> minimal information is:
>>
>> column 1: chromosome
>> column 2: start
>> column 3: end
>> column 6: orientation, either 'plus', 'minus' or undefined. (in this case
>> a '+')
>>
>> Is there any compact container to load, say, 50 million records? I
>> thought that RangedData could do that but after reading the
>> documentation I see that it does not hold strand information.
>>
>> If there is such container, how do you load it up from a BED file?
>>
>> Thank you,
>>
>> Ivan
>>
>> Ivan Gregoretti, PhD
>> National Institute of Diabetes and Digestive and Kidney Diseases
>> National Institutes of Health
>> 5 Memorial Dr, Building 5, Room 205.
>> Bethesda, MD 20892. USA.
>> Phone: 1-301-496-1592
>> Fax: 1-301-496-9878
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>
>