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  • 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

  • #2
    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.

    Comment


    • #3
      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 ?

      Comment

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