Annotating a PWM

Hi all,

I have made a PWM from some bigWig files of DNase coverage data and a TF binding site list across mm10. I would like to get annotation of this PWM in a separate file and not exactly sure how to do this. Any help would be great thanks.

Rob

pwm dnase-seq

• 1,653 views • link

written 9.5 years ago by rbronste

0 answers

No answers yet.

More posts like this

Extracting Enhancer Regions from ENCODE Annotation Files
written 2.3 years ago by YamengWu •

Hi there, I’m looking for help on how to access enhancer regions from ENCODE annotation files. I’m researching the enhancers in the human heart. I …
Annotate the K-mers of same length with TFs
written 6.1 years ago by ancient_learner

Hi, Greetings! I have a list of K-mers (Human) like below AAGTGCG GGCGGCT ACGTGGCA TGCGTGGG TGGCGTGA Some of these K-mers may be serving as binding …
plotHeatmap for clustering samples
written 6.2 years ago by jamzaleg84 •

Hello Everyone, I've been using deeptools to make heatmaps of ChIP-seq samples and hierarchical clustering of those samples. I have two different transcription factors that …
Transcription factor binding sites in cancer
written 6.9 years ago by caokai001 •

Hello everyone! For Human,We know that there are many `snp` in cancer cell, we have `SNP` and `ATAC-seq data` of this cancer, and obtained TF …
Find Transcription factor binding site for a gene list
written 7.9 years ago by salvatore.raieli2

Hi everyone, I have a list of genes that are different expressed between tumor and normal tissue. I have two drugs that block two different …
Bed to BAM information transfer
written 9.4 years ago by rbronste

Hi, Wondering about the validity of converting bed to BAM, for instance in terms of TF foot printing...if lets say Ive done some analysis and …
Alternative to PWMtools
written 9.5 years ago by rbronste

Hi, I am looking for a faster alternative to PWMtools, which is useful on the small scale but doesn't get the job done with large …
CENTIPEDE DNase-seq analysis - ylist question
written 9.5 years ago by rbronste

Hi All, Trying to use CENTIPEDE to infer TF footprints. I made a PWM using bwtool of one meme TF matrix and my bigWig files …
bwtool matrix error - invalid signed integer
written 9.5 years ago by rbronste

Hi all, I am using bwtool to make a matrix for footprinting a TF using a BED file I generated with meme and some bigwig …
how to interpret scores from a PWM match
written 11.6 years ago by Affan

I created a PWM using true binding sites from Riken 4 database, hg 18. To test my PWM, I picked a random true binding site …