Files | Path |
---|---|
Alignment | |
Replicate 1 | |
Filtered & deduped bam | ./align/rep1/Polstein2015_Rep5_trimmed.nodup.bam |
Fastq | |
Bam | ./align/rep1/Polstein2015_Rep5_trimmed.bam |
Tag-align | ./align/rep1/Polstein2015_Rep5_trimmed.nodup.tagAlign.gz |
Pseudo-replicates | |
Replicate 1 | |
Pseudo-replicate 1 | |
Tag-align | ./align/pseudo_reps/rep1/pr1/Polstein2015_Rep5_trimmed.nodup.pr1.tagAlign.gz |
Pseudo-replicate 2 | |
Tag-align | ./align/pseudo_reps/rep1/pr2/Polstein2015_Rep5_trimmed.nodup.pr2.tagAlign.gz |
QC and logs | |
Replicate 1 | |
Bowtie2 map. log | ./qc/rep1/Polstein2015_Rep5_trimmed.align.log |
Dedup. log | ./qc/rep1/Polstein2015_Rep5_trimmed.dup.qc |
Cross-corr. plot | ./qc/rep1/Polstein2015_Rep5_trimmed.nodup.25M.cc.plot.pdf |
  | Total Reads | % Aligned |
---|---|---|
rep1 | 28916104 | 99.70 |
  | Unpaired Reads | Paired Reads | Unmapped Reads | Unpaired Dupes | Paired Dupes | Paired Opt. Dupes | % Dupes |
---|---|---|---|---|---|---|---|
rep1 | 19481112 | 0 | 0 | 513092 | 0 | 0 | 0.026338 |
  | Reads (QC-passed) | Reads (QC-failed) | Dupes (QC-passed) | Dupes (QC-failed) | Mapped Reads | % Mapped |
---|---|---|---|---|---|---|
rep1 | 18968020 | 0 | 0 | 0 | 18968020 | 100.00 |
  | Total Read Pairs | Distinct Read Pairs | One Read Pair | Two Read Pairs | NRF = Distinct/Total | PBC1 = OnePair/Distinct | PBC2 = OnePair/TwoPair |
---|---|---|---|---|---|---|---|
rep1 | 19450139 | 18957962 | 18523451 | 392541 | 0.974695 | 0.977080 | 47.188576 |
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
  | numReads | estFragLen | corr_estFragLen | PhantomPeak | corr_phantomPeak | argmin_corr | min_corr | NSC | RSC |
---|---|---|---|---|---|---|---|---|---|
rep1 | 18957962 | 0 | 0.239605365068555 | 20 | 0.2384917 | 1500 | 0.2018288 | 1.187171 | 1.030376 |
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