<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>

CC BY-SA 4.0
2020-11-20T08:07:02.860Z
Usually downstream programs will take sequencing depth differences into account for you, so you only need to downsample if you get really funky results.
Devon Ryan
CC BY-SA 4.0
2020-11-20T08:59:20.217Z
"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 ?
kcm
CC BY-SA 4.0
2020-11-20T17:59:21.677Z
control is almost always better than IgG. For this reason don’t bother with IgG.
Devon Ryan
<chip-seq>
Chip-seq down-sampling problem
# 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.  

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## 0 answers

