Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • StephaniePi83
    replied
    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 ?

    Leave a comment:


  • Kennels
    replied
    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.

    Leave a comment:


  • 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

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:58 AM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 02:20 PM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-07-2024, 06:58 AM
0 responses
181 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-06-2024, 08:18 AM
0 responses
230 views
0 likes
Last Post seqadmin  
Working...
X