SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
repeating chipseq or chipseq with another antibody hawainpanda Sample Prep / Library Generation 2 03-12-2015 04:56 PM
Quantifying copies of a single locus robinweide Bioinformatics 0 10-17-2014 03:28 PM
Quantifying ChIP-seq signal from wiggle file polvo Bioinformatics 2 12-10-2013 11:53 PM
Indexing ChIPseq libraries using Illumina's TruSeq and ChIPseq kits Alex Clop Epigenetics 6 11-08-2012 12:07 PM
ChIPseq wig file with the input subtracted from ChIP sample abmmki Illumina/Solexa 1 08-02-2012 06:51 PM

Reply
 
Thread Tools
Old 04-20-2016, 06:48 AM   #1
kajot
Member
 
Location: Germany

Join Date: Dec 2013
Posts: 16
Default Quantifying ChIPseq signal for one sample

Hey Everybody,

I am trying to rank genes according to their phosphorylated CTD Pol II occupancy as a rough estimate of ongoing transcription.

I am using ENCODE Pol2 ChIPseq data, which means I have access to called peaks, raw and wiggle files. I would like to ask you if it's generally a good strategy to quantify signal from bigWig file using bigWigAverageOverBed UCSC tool for all the human genes in given cell line. I avoided using called narrow peaks in this case, as I believe this would approximate the polymerase stalling better than the actual transcription.

To assess this approach, I am correlating this quantified signal to RNAseq RPKM values from the same cell line and get Spearman correlation coefficient of around 0.62.

Is there a better way to rank genes by their ChIPseq signal in a single sample?


Thanks for any suggestions,
K.
kajot is offline   Reply With Quote
Old 04-20-2016, 07:16 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Something along those lines should work. We normally use computeMatrix from deepTools for this sort of purpose, but if you only want a single value then bigWigAverageOverBed should give equivalent results.
dpryan is offline   Reply With Quote
Old 04-21-2016, 08:30 AM   #3
kajot
Member
 
Location: Germany

Join Date: Dec 2013
Posts: 16
Default

As always very helpful, Devon, I owe you few beers already

Thanks for the tip!
kajot is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:46 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO