Body: <p><strong>Control sample chip read stat</strong></p>
  <pre><code>56234445 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  55173337 + 0 mapped (98.11% : N/A)
  56234445 + 0 paired in sequencing
  28078024 + 0 read1
  28156421 + 0 read2
  53808040 + 0 properly paired (95.69% : N/A)
  54626508 + 0 with itself and mate mapped
  546829 + 0 singletons (0.97% : N/A)
  162718 + 0 with mate mapped to a different chr
  112602 + 0 with mate mapped to a different chr (mapQ&gt;=5)
  </code></pre>
  <p><strong>IgG sample chip seq read stat</strong></p>
  <pre><code>32745255 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  31546173 + 0 mapped (96.34% : N/A)
  32745255 + 0 paired in sequencing
  16362391 + 0 read1
  16382864 + 0 read2
  30934194 + 0 properly paired (94.47% : N/A)
  31269484 + 0 with itself and mate mapped
  276689 + 0 singletons (0.84% : N/A)
  79786 + 0 with mate mapped to a different chr
  49658 + 0 with mate mapped to a different chr (mapQ&gt;=5)
  </code></pre>
  <p><strong>knockout sample Rep 1 stat</strong></p>
  <pre><code>28044731 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  27459222 + 0 mapped (97.91% : N/A)
  28044731 + 0 paired in sequencing
  14014483 + 0 read1
  14030248 + 0 read2
  26685254 + 0 properly paired (95.15% : N/A)
  27162846 + 0 with itself and mate mapped
  296376 + 0 singletons (1.06% : N/A)
  116684 + 0 with mate mapped to a different chr
  88965 + 0 with mate mapped to a different chr (mapQ&gt;=5)
  </code></pre>
  <p><strong>Knockout sample rep 2 stat</strong></p>
  <pre><code>32410094 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  31774629 + 0 mapped (98.04% : N/A)
  32410094 + 0 paired in sequencing
  16196814 + 0 read1
  16213280 + 0 read2
  30802808 + 0 properly paired (95.04% : N/A)
  31561218 + 0 with itself and mate mapped
  213411 + 0 singletons (0.66% : N/A)
  89688 + 0 with mate mapped to a different chr
  63838 + 0 with mate mapped to a different chr (mapQ&gt;=5)
  </code></pre>
  <p>Do i need to down-sample with respect to the IgG for control sample which has lot more reads at the same time Knockout sample 1 has less read. So is it good to go for further analysis or i need to down sample them ?</p>
  <p>Any suggestion is really appreciated</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-20T08:07:02.860Z
Comments.Text: Usually downstream programs will take sequencing depth differences into account for you, so you only need to downsample if you get really funky results.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-20T08:59:20.217Z
Comments.Text: "if you get really funky results." i did plot using your deeptools i do see a small peak in IgG  so i feel there might be some issue.. which one would be better IgG or input im not clear .for the comparison ..any insight if IgG would be better or input ?
Comments.UserDisplayName: kcm
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-20T17:59:21.677Z
Comments.Text: control is almost always better than IgG. For this reason don’t bother with IgG.
Comments.UserDisplayName: Devon Ryan
Tags: <chip-seq>
Title: Chip-seq down-sampling problem
ThreadText: # Chip-seq down-sampling problem
  
  (Asked by: username_0 on 2020-11-20)
  
  **Control sample chip read stat**
  
  ```
  56234445 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  55173337 + 0 mapped (98.11% : N/A)
  56234445 + 0 paired in sequencing
  28078024 + 0 read1
  28156421 + 0 read2
  53808040 + 0 properly paired (95.69% : N/A)
  54626508 + 0 with itself and mate mapped
  546829 + 0 singletons (0.97% : N/A)
  162718 + 0 with mate mapped to a different chr
  112602 + 0 with mate mapped to a different chr (mapQ>=5)
  
  ```
  
  **IgG sample chip seq read stat**
  
  ```
  32745255 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  31546173 + 0 mapped (96.34% : N/A)
  32745255 + 0 paired in sequencing
  16362391 + 0 read1
  16382864 + 0 read2
  30934194 + 0 properly paired (94.47% : N/A)
  31269484 + 0 with itself and mate mapped
  276689 + 0 singletons (0.84% : N/A)
  79786 + 0 with mate mapped to a different chr
  49658 + 0 with mate mapped to a different chr (mapQ>=5)
  
  ```
  
  **knockout sample Rep 1 stat**
  
  ```
  28044731 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  27459222 + 0 mapped (97.91% : N/A)
  28044731 + 0 paired in sequencing
  14014483 + 0 read1
  14030248 + 0 read2
  26685254 + 0 properly paired (95.15% : N/A)
  27162846 + 0 with itself and mate mapped
  296376 + 0 singletons (1.06% : N/A)
  116684 + 0 with mate mapped to a different chr
  88965 + 0 with mate mapped to a different chr (mapQ>=5)
  
  ```
  
  **Knockout sample rep 2 stat**
  
  ```
  32410094 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  31774629 + 0 mapped (98.04% : N/A)
  32410094 + 0 paired in sequencing
  16196814 + 0 read1
  16213280 + 0 read2
  30802808 + 0 properly paired (95.04% : N/A)
  31561218 + 0 with itself and mate mapped
  213411 + 0 singletons (0.66% : N/A)
  89688 + 0 with mate mapped to a different chr
  63838 + 0 with mate mapped to a different chr (mapQ>=5)
  
  ```
  
  Do i need to down-sample with respect to the IgG for control sample which has lot more reads at the same time Knockout sample 1 has less read. So is it good to go for further analysis or i need to down sample them ?
  
  Any suggestion is really appreciated
  
  **Tags:** chip-seq
  
  > **Comments:**
  > **username_1**: Usually downstream programs will take sequencing depth differences into account for you, so you only need to downsample if you get really funky results.  
  > **username_0**: "if you get really funky results." i did plot using your deeptools i do see a small peak in IgG  so i feel there might be some issue.. which one would be better IgG or input im not clear .for the comparison ..any insight if IgG would be better or input ?  
  > **username_1**: control is almost always better than IgG. For this reason don’t bother with IgG.  
  
  ---
  
  ## 0 answers
  
  