Title: ZBTB17_MACS2

Report generated at Thu Apr 13 19:19:34 PDT 2017

Command line arguments

-title ZBTB17_MACS2 -nth 5 -species hg38_ENCODE -url_base http://mitra.stanford.edu/kundaje/leepc12/imk_chipseq/ZBTB17_MACS2/out -filt_bam1 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep1/ENCFF057NJA.bam -filt_bam2 /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/ZBTB17_MACS2/out/align/rep2/ENCFF078YAS.bam -ctl_tag /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz -pe -histone

Pipeline version

Latest git commit SHA1: 3e6c43ca5035c8766d19e6245573946c380bb5a8 (Sat Apr 8 15:37:52 2017)


Directories and files
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FilesPath
Alignment
Replicate 1
Filtered & deduped bam ./align/rep1/ENCFF057NJA.bam
Tag-align ./align/rep1/ENCFF057NJA.tagAlign.gz
Replicate 2
Filtered & deduped bam ./align/rep2/ENCFF078YAS.bam
Tag-align ./align/rep2/ENCFF078YAS.tagAlign.gz
Control 1
Tag-align /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeOtherZnfData/Encode3Datahg38/InputData/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Pooled replicate
Tag-align ./align/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign.gz
Pooled pseudo-replicates
Pooled pseudo-replicate 1
Tag-align ./align/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign.gz
Pooled pseudo-replicate 2
Tag-align ./align/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign.gz
Signal tracks
MACS2
Replicate 1
P-value ./signal/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
Replicate 2
P-value ./signal/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
Pooled replicate
P-value ./signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.pval.signal.bw
Fold enrichment ./signal/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.fc.signal.bw
Peaks
MACS2
Replicate 1
Narrow peak ./peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/rep1/ENCFF057NJA.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Replicate 2
Narrow peak ./peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/rep2/ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Pooled replicate
Narrow peak ./peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_rep/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep1/pr1/ENCFF057NJA.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Pseudo-replicate 2
Narrow peak ./peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep1/pr2/ENCFF057NJA.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Replicate 2
Pseudo-replicate 1
Narrow peak ./peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep2/pr1/ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Pseudo-replicate 2
Narrow peak ./peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pseudo_reps/rep2/pr2/ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Pooled pseudo-replicate
Pooled pseudo-replicate 1
Narrow peak ./peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_pseudo_reps/ppr1/ENCFF057NJA.pr1_ENCFF078YAS.pr1.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Pooled pseudo-replicate 2
Narrow peak ./peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.narrowPeak.gz
Broad peak ./peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.broadPeak.gz
Gapped peak ./peak/macs2/pooled_pseudo_reps/ppr2/ENCFF057NJA.pr2_ENCFF078YAS.pr2.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.gappedPeak.gz
Naive overlap
Broad peak ./peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.broadPeak.gz
Gapped peak ./peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.gappedPeak.gz
Peak ./peak/macs2/overlap/ENCFF057NJA_ENCFF078YAS.tagAlign_x_ss_50M_2000_GRCh38.nodup.tagAlign.naive_overlap.filt.narrowPeak.gz
QC and logs
Replicate 1
Cross-corr. log ./qc/rep1/ENCFF057NJA.15M.cc.qc
Cross-corr. plot ./qc/rep1/ENCFF057NJA.15M.cc.plot.pdf
Replicate 2
Cross-corr. log ./qc/rep2/ENCFF078YAS.15M.cc.qc
Cross-corr. plot ./qc/rep2/ENCFF078YAS.15M.cc.plot.pdf

Visualization
Visualize  JSON (datahub)

Workflow diagram (g. peak : gapped peak from MACS2, n. peak : narrow peak from MACS2, r. peak : region peak from SPP)


Enrichment QC (strand cross-correlation measures)
 rep1
rep2
Reads1500000015000000
Est. Fragment Len.265245
Corr. Est. Fragment Len.0.2133032121125590.212565948653747
Phantom Peak105105
Corr. Phantom Peak0.2041990.2045879
Argmin. Corr.15001500
Min. Corr.0.18032940.1791742
NSC1.1828531.186365
RSC1.3814151.313926

NOTE: One end of each read-pair is randomly selected and the reads are then randomly subsampled to a max of 15M


rep1
 
rep2