How can I check library diversity in ChIPSeq data ?
1 answer
I would have a look at (more or less in this order):
- FastQC report for overrepresented kmers, sequences and adapter contamination
- Picard tools, particular EstimateLibraryComplexity and MarkDuplicates for duplication rate
- deepTools, bamFingerprint is quite handy to assess the level of enrichment
However, I think most of the statistics reported by these tools are meaningful if you have a prior idea of what a good library would look like. In the case of ChIP-Seq it might depend on what you are ChIP'ing.
Log in to answer this question.
More posts like this
-
Tools for assigning putative enhacers to respective genes
written by alejandrocastillaibeas •
-
Tool for detecting valleys in Chip-seq like data?
written by kxk302 •
-
Nanopore tutorial for beginners
written by Lila M
-
Identifying peaks of similar enrichment from ChIP-seq?
written by umbch •
-
Compare ChIP-seq data from various experiments
written by bharath.mh24 •
-
Tools to identify enhancers from chromatin marks
written by guiu
-
How To Query The Human Chipseq Data (Encode) For A Transcription Factor Binding To A Specific Gene …
written by Ashutosh Pandey
-
Chip-Seq Peak Caller Able To Find Peaks Split By Indels?
written by 2184687-1231-83-
-
How About Starting A Tutorial For Chip Seq Data Analysis?
written by Dataminer
-
Transcriptome Assembly Of Illumina Reads On Low-Mem Machines?
written by 2184687-1231-83-
