| Alignment |
|
| Replicate 1 |
|
| Filtered & deduped bam | ./align/rep1/ZNF41.rep1.bam
|
| Tag-align | ./align/rep1/ZNF41.rep1.tagAlign.gz
|
| Replicate 2 |
|
| Filtered & deduped bam | ./align/rep2/ZNF41.rep2.bam
|
| Tag-align | ./align/rep2/ZNF41.rep2.tagAlign.gz
|
| Control 1 |
|
| Tag-align |
|
| Pooled replicate |
|
| Tag-align | ./align/pooled_rep/ZNF41.rep1_ZNF41.rep2.tagAlign.gz
|
| Pseudo-replicates |
|
| Replicate 1 |
|
| Pseudo-replicate 1 |
|
| Tag-align | ./align/pseudo_reps/rep1/pr1/ZNF41.rep1.pr1.tagAlign.gz
|
| Pseudo-replicate 2 |
|
| Tag-align | ./align/pseudo_reps/rep1/pr2/ZNF41.rep1.pr2.tagAlign.gz
|
| Replicate 2 |
|
| Pseudo-replicate 1 |
|
| Tag-align | ./align/pseudo_reps/rep2/pr1/ZNF41.rep2.pr1.tagAlign.gz
|
| Pseudo-replicate 2 |
|
| Tag-align | ./align/pseudo_reps/rep2/pr2/ZNF41.rep2.pr2.tagAlign.gz
|
| Pooled pseudo-replicates |
|
| Pooled pseudo-replicate 1 |
|
| Tag-align | ./align/pooled_pseudo_reps/ppr1/ZNF41.rep1.pr1_ZNF41.rep2.pr1.tagAlign.gz
|
| Pooled pseudo-replicate 2 |
|
| Tag-align | ./align/pooled_pseudo_reps/ppr2/ZNF41.rep1.pr2_ZNF41.rep2.pr2.tagAlign.gz
|
| Signal tracks |
|
| MACS2 |
|
| Pooled replicate |
|
| P-value | ./signal/macs2/pooled_rep/ZNF41.rep1_ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.pval.signal.bw
|
| Fold enrichment | ./signal/macs2/pooled_rep/ZNF41.rep1_ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.fc.signal.bw
|
| Peaks |
|
| SPP |
|
| Pooled Replicate |
|
| Region peak | ./peak/spp/pooled_rep/ZNF41.rep1_ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
|
| Replicate 1 |
|
| Region peak | ./peak/spp/rep1/ZNF41.rep1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
|
| Replicate 2 |
|
| Region peak | ./peak/spp/rep2/ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
|
| Pooled pseudo-replicates |
|
| Pooled pseudo-replicate 1 |
|
| Region peak | ./peak/spp/pooled_pseudo_reps/ppr1/ZNF41.rep1.pr1_ZNF41.rep2.pr1.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
|
| Pooled pseudo-replicate 2 |
|
| Region peak | ./peak/spp/pooled_pseudo_reps/ppr2/ZNF41.rep1.pr2_ZNF41.rep2.pr2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.regionPeak.gz
|
| Naive overlap |
|
| Peak | ./peak/spp/overlap/ZNF41.rep1_ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.naive_overlap.filt.regionPeak.gz
|
| MACS2 |
|
| Pooled replicate |
|
| Narrow peak | ./peak/macs2/pooled_rep/ZNF41.rep1_ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.narrowPeak.gz
|
| Broad peak | ./peak/macs2/pooled_rep/ZNF41.rep1_ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.broadPeak.gz
|
| Gapped peak | ./peak/macs2/pooled_rep/ZNF41.rep1_ZNF41.rep2.tagAlign_x_input15MReadsNSCLess1.05.50MSubsample.tagAlign.gappedPeak.gz
|
| IDR |
|
| True replicates |
|
| Rep. 1 vs. Rep. 2 |
|
| IDR peak | ./peak/idr/true_reps/rep1-rep2/ZNF41_rep1-rep2.IDR0.05.filt.narrowPeak.gz
|
| Pooled pseudo-replicates |
|
| IDR peak | ./peak/idr/pooled_pseudo_reps/ZNF41_ppr.IDR0.05.filt.narrowPeak.gz
|
| Optimal set |
|
| IDR peak | ./peak/idr/optimal_set/ZNF41_ppr.IDR0.05.filt.narrowPeak.gz
|
| Conservative set |
|
| IDR peak | ./peak/idr/conservative_set/ZNF41_rep1-rep2.IDR0.05.filt.narrowPeak.gz
|
| QC and logs |
|
| Replicate 1 |
|
| Cross-corr. log | ./qc/rep1/ZNF41.rep1.15M.cc.qc
|
| Cross-corr. plot | ./qc/rep1/ZNF41.rep1.15M.cc.plot.pdf
|
| Replicate 2 |
|
| Cross-corr. log | ./qc/rep2/ZNF41.rep2.15M.cc.qc
|
| Cross-corr. plot | ./qc/rep2/ZNF41.rep2.15M.cc.plot.pdf
|
| IDR |
|
| IDR QC log | ./qc/ZNF41_IDR_final.qc
|
| True replicates |
|
| Rep. 1 vs. Rep. 2 |
|
| IDR plot | ./peak/idr/true_reps/rep1-rep2/ZNF41_rep1-rep2.unthresholded-peaks.txt.png
|
| Pooled pseudo-replicates |
|
| IDR plot | ./peak/idr/pooled_pseudo_reps/ZNF41_ppr.unthresholded-peaks.txt.png
|
