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Old 10-02-2013, 07:55 AM   #1
StephaniePi83
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Location: France

Join Date: Sep 2011
Posts: 52
Default plotting small RNA using window size - step size

Dear all,
I'm analyzing small RNA seq data.
I have the genomic coordinates of some elements (called cluster) on the genome.
I have to make some graph, representing the density of small RNA mapping to these cluster using a windows size of 250nt and step size of 25 nt ( i have to do this because it has already been done in a paper).
I'm not sure to well understand :
does it mean that i have to created a BED file called windows.bed for 250nt windows across the element of interest and that each windows overlap by 25 nt.
For example :

Code:
chr1 0 250
chr1 225 475
....
and i create a 2nd bed file of sequence reads called reads.bed

And i can use coverageBed from Bedtools to calculate for each window in windows.bed the number of reads in reads.bed that overlap the window.

Do i well understand the notion of window size / step size ?

Thanks in advance for your help,
Stéph

and then, i can use Bedtools
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Old 10-02-2013, 04:58 PM   #2
Kennels
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Location: Sydney

Join Date: Feb 2011
Posts: 149
Default

Quote:
Originally Posted by StephaniePi83 View Post
Dear all,
I'm analyzing small RNA seq data.
I have the genomic coordinates of some elements (called cluster) on the genome.
I have to make some graph, representing the density of small RNA mapping to these cluster using a windows size of 250nt and step size of 25 nt ( i have to do this because it has already been done in a paper).
I'm not sure to well understand :
does it mean that i have to created a BED file called windows.bed for 250nt windows across the element of interest and that each windows overlap by 25 nt.
For example :

Code:
chr1 0 250
chr1 225 475
....
and i create a 2nd bed file of sequence reads called reads.bed

And i can use coverageBed from Bedtools to calculate for each window in windows.bed the number of reads in reads.bed that overlap the window.

Do i well understand the notion of window size / step size ?

Thanks in advance for your help,
Stéph

and then, i can use Bedtools
Hi,

For example, it means you count the number of small RNA that mapped to pos 0-250, then 25-275, then 50-300 and so on, and you plot the total number of mapped smallRNA in these 250nt bins.
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Old 10-03-2013, 12:00 AM   #3
StephaniePi83
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Location: France

Join Date: Sep 2011
Posts: 52
Default

Hi Kennels,
I'm not sure to well understand, what is the x-axis of the plot ? [0,25,50, ...] ?
There is redundancy no ? I mean, small RNA that have been counted in the windows [0,250] will also be counted in the windows [25,275], no ?
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