Remove Blacklist regions from ChIP-seq Data

Question

[Ulduz]

Hi,

In order to get rid of false positive peaks, I want to filter out blacklist region after alignment with Bowtie... I've search and there are three different bed files for Blacklist regions. So which of them is the best choice for TF ChIP-seq data?

http://www.broadinstitute.org/~anshul/projects/encode/rawdata/blacklists/hg19-blacklist-README.pdf

And do you filter them out with intersect from Bedtools?

[ATCG]

were you able to solve this problem? I need to do the same and will appreciate your feedback,

[ATCG]

were you able to filter the blacklisted regions with intersect from Bedtools? In order to use bedops you need to convert the bam file to bed filter and than convert the back to bam, I was able to do the filtering, but unable to convert the bed to bam file using bedtools bedtobam option any feedback would be greatly appreciated. thanks!!

Answer 1

[Alex Reynolds]

Once you have picked your blacklists, one way to filter is with BEDOPS bedops -n:

$ bedops -n -1 all_peaks.bed blacklist_regions.bed > filtered_peaks.bed<

The -1 option indicates a minimum threshold of one base of overlap required to apply the filter operation (basically, any overlap).

[ATCG]

I have an input sample with high Kmer content, and no peaks are found in my IP samples (3replicates) when I use this input. On these same IP samples I do find peaks when using a baseline treatment input and also when I call peaks not using an input at all.

my input sample has the following Kmer Content:

Sequence    Count   PValue  Obs/Exp Max Max Obs/Exp Position
AGGGGGG 13010   0.0 15.102037   1
TCGCGTA 345 1.1974935E-6    11.862445   37
TGGGGGG 25385   0.0 11.1068325  1
CGCCTGA 4925    0.0 9.191745    21
TATGCCG 2045    0.0 8.6882925   42
CGCGTAT 450 2.8213963E-4    8.33926 38
TCTCCCG 7310    0.0 7.170219    16
CGTATGC 2500    0.0 6.691238    40
CTCGTAT 2440    0.0 6.431545    38
ACACGTC 4290    0.0 6.4261694   9
TGCCGTC 3070    0.0 6.3503175   44
CGTCTGA 4360    0.0 6.3229723   12
TCCCGCC 9155    0.0 5.985545    18
CATCGCG 970 2.6135147E-5    5.974066    35
CTCCCGC 9090    0.0 5.728751    17
TCTCGTA 2575    0.0 5.695125    37
GCCGTCT 3315    0.0 5.2648993   45
CCGCCTG 10365   0.0 5.1227307   20
ATGCCGT 3405    0.0 5.120038    43
ACGTCTG 6060    0.0 5.0546627   11