Pipeline version (latest git commit SHA1):ba549bcd70f73d261f452659301ef1ae1a1ae4ff (Mon Jan 30 20:26:58 2017)

Directories and files
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FilesPath
Alignment
Replicate 1
Filtered & deduped bam
Tag-align ./align/rep1/CTCF-Antibody.Rep1.nodup.tagAlign.gz
Replicate 2
Filtered & deduped bam
Tag-align ./align/rep2/CTCF-Antibody.Rep2.nodup.tagAlign.gz
Control 1
Filtered & deduped bam
Tag-align ./align/ctl1/CTCF-Antibody.ctl.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep1/pr1/CTCF-Antibody.Rep1.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep1/pr2/CTCF-Antibody.Rep1.nodup.pr2.tagAlign.gz
Replicate 2
Pseudo-replicate 1
Tag-align ./align/pseudo_reps/rep2/pr1/CTCF-Antibody.Rep2.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align ./align/pseudo_reps/rep2/pr2/CTCF-Antibody.Rep2.nodup.pr2.tagAlign.gz
QC and logs
Replicate 1
Cross-corr. log ./qc/rep1/CTCF-Antibody.Rep1.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep1/CTCF-Antibody.Rep1.nodup.15M.cc.plot.pdf
Replicate 2
Cross-corr. log ./qc/rep2/CTCF-Antibody.Rep2.nodup.15M.cc.qc
Cross-corr. plot ./qc/rep2/CTCF-Antibody.Rep2.nodup.15M.cc.plot.pdf

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


Cross-correlation QC (all)
 numReadsestFragLencorr_estFragLenPhantomPeakcorr_phantomPeakargmin_corrmin_corrNSCRSC
rep1
103978261100.422063186386812400.317679215000.096425734.3770811.471785
rep2
48039041150.207286177158335400.148989615000.058172343.5633121.64191

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value
Important columns highlighted, but all/whole file can be stored for display


rep1
 
rep2