Question: Remove Blacklist regions from ChIP-seq Data
2
gravatar for Ulduz
5.6 years ago by
Ulduz20
Istanbul
Ulduz20 wrote:

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?

chip-seq • 5.2k views
ADD COMMENTlink modified 5.6 years ago by Alex Reynolds30k • written 5.6 years ago by Ulduz20

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

ADD REPLYlink written 4.0 years ago by DataFanatic230

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!!

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by DataFanatic230
4
gravatar for Alex Reynolds
5.6 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

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).

ADD COMMENTlink modified 9 months ago by RamRS27k • written 5.6 years ago by Alex Reynolds30k

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
ADD REPLYlink modified 9 months ago by RamRS27k • written 4.0 years ago by DataFanatic230
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