Aligning ChIP-seq reads to repeats: IgG vs input controls
I would like to check if I have ChIP-seq reads that map to repeats in the genome (e.g. LINEs, SINEs, telomeres, centromeres etc.) I use the Kharchenko lab repeat aligner to do this.
I intuitively feel as if an Input sequencing control is the best control since this should give an idea of the copy number of repeats within a single genome. However, I have noticed that some people use an IgG control instead.
Are there any thoughts on which control is better for alignments to repeats specifically?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
What is the different bewteen ucsc simple repeat and tandem repeat
written by octpus616 •
-
can we use the same aligner to map reads obtained from ChIP-seq and RNA-seq expriments to the refer…
written by yingshanwang1999 •
-
ChIP-Seq. plotFingerprint interpretation: 2 ChIPs are like IgG control. Conclusions?
written by KB* •
-
Looking for recommendation: What tool can I use to reliably generate Transposable elements from a G…
written by jaqx008
-
How to annotate repeats?
written by Zee_S
-
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
written by gil.hornung
-
RepeatModeler and RepeatMasker for non-model species
written by nancydong20
-
Where are examples of Interspersed repeats?
written by veronicaschroeder78
-
Removal of repeat and blacklist regions from ChIP-seq data
written by James Ashmore
-
What Control For Chip-Seq: Input, Igg Or Untagged Strain?
written by Olbzn •
