Unusual Chipseq Data
HI, I am looking at some ChIPSeq data that is rather unusual. The forward and reverse read form deep thin stacks. Their width is mostly just above the read length of 75 bp. The 'peaks' (pseudo-peaks?) are distributed well across the mouse genome. Have any of you see this? What could be the reason? This experiment is investigating transcription factor binding ....
Thanks! Jarus
• 2,028 views
•
link
updated
by
Sean Davis
•
written
by
Jarus •
•
written
by
Jarus •
1 answer
It sounds like you might have a problem with PCR duplicates. This might arise because of inadequate starting DNA, for example. A thorough QC evaluation and perhaps some forensic bioinformatics are probably warranted before proceeding with your analysis.
• 0 views
•
link
written
by
Sean Davis
Log in to answer this question.
More posts like this
-
Question about constructing a consensus peak file for diffTF
written by lilithslily •
-
merging of two assemblies from different short-reads techniques
written by Andrew Yu •
-
Bedtools Fisher Genome File
written by megannj •
-
Presence of both forward and reverse motifs in transcription factor binding sites
written by jjl5sw •
-
Can I use AME - Analysis of Motif Enrichment - for RNA-Seq data?
written by Chris Gene
-
Where are the actual transcription factor binding sites located in the CHIP-seq peaks
written by Saad Khan
-
encode project .bb annotation files
written by janeshen91 •
-
interpreting FIMO results - p value and q value
written by Affan
-
Using Homer Programs For Denovo Motif : Different Results Among Its Own Versions
written by RT •
-
Poly(A) Signal Prediction And Forward/Reverse Strand Conventions
written by Lídia •
