how to extract all signal value from chip seq data for a particular k-mer

I want to find a particular 8 mer from a chip-seq data (e.g. coordinates) and their associated signal value. I want to use this information to compare binding affinity of each 8 mer for that transcription factor. Any suggestion would be greatly appreciated

chip-seq k mer

• 1,609 views • link

written 10.4 years ago by jye •

0 answers

No answers yet.

More posts like this

Normalizing chip-seq signals with different number of peaks
written 3.5 years ago by Rajendra KC •

Hello all, I want to compare chip-seq signals of polymerase1 and polymerase3 over few bed coordinates but I guess I must be normalizing these chip-seq …
Integrate chip-seq with rna-seq?
written 4.2 years ago by Tonkatsu •

How would one go about associating Chip-seq data (from encode) with rna-seq differentially expressed genelists? In particular, whether certain differentially expressed genes are associated with …
Differential binding ChIP-seq/RNA-seq analysis
written 7.5 years ago by dcheng1 •

Hi! I want to do some cell-type-specific analysis using ChIP-seq. I want to **find a list of ChIP-seq peaks locations that are specific to cell …
How to interpret ChIP-seq peak at cell line level?
written 8.1 years ago by Yijun Tian •

Hello everyone, I have a list of enriched peaks called from rigorous prepared ChIP-seq reads obtained by certain treatment which can activate specific transcription factor. …
What is the best method ChIPseq differential binding analysis?
written 8.5 years ago by biopat •

Hi all, I want to quantitatively compare ChIP-seq data! Experimental condition: - same background cell line but samples differ (WT, KO1) - same antibody was …
Finding specific k-mer in human genome
written 10.4 years ago by jye •

I want to find a specific 9-mer (GATCGATGC) in human genome, and then export them into a bed file with all information including chromosome, start …
Which tool can plot the enrichment of specified motif across ChIP-seq bed files?
written 11.3 years ago by xiaoyonf •

Hi, I have two ChIP-seq bed files of same transcription factor. I want to compare one specific binding motif between these two ChIP-seq binding peaks, …
how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?
written 11.7 years ago by liu4gre

I just learn to understanding ENCODE ChiP-Seq data for Transcription Factor binding. I know the narrowPeak format consists BED6+4 columns which is described in https://genome.ucsc.edu/FAQ/FAQformat.html#format12. …
how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?
written 11.8 years ago by liu4gre

I just learn to understanding ENCODE ChiP-Seq data for Transcription Factor binding. I know the narrowPeak format consists BED6+4 columns which is described in https://genome.ucsc.edu/FAQ/FAQformat.html#format12. …
NarrowPeak format of ChiP-seq
written 12.2 years ago by liu4gre

I just learn to understanding ENCODE ChiP-Seq data for Transcription Factor binding. I looked at the narrowpeak files and find there is a column named …