CEBPB ChIP-seq on human A549 produced by the Snyder lab
Pipeline version
v1.2.2
Genome
hg38_google.tsv
Paired-end per replicate
[False, False]
Aligner
bowtie2
Peak caller
spp
Control paired-end per replicate
[False, False]
Alignment quality metrics
SAMstat (raw BAM)
rep1
rep2
ctl1
ctl2
Total
30537463
23711730
24114469
28739630
Total(QC-failed)
0
0
0
0
Dupes
0
0
0
0
Dupes(QC-failed)
0
0
0
0
Mapped
30231793
23191870
23861084
27460091
Mapped(QC-failed)
0
0
0
0
% Mapped
0.0
0.0
0.0
0.0
Paired
0
0
0
0
Paired(QC-failed)
0
0
0
0
Read1
0
0
0
0
Read1(QC-failed)
0
0
0
0
Read2
0
0
0
0
Read2(QC-failed)
0
0
0
0
Properly Paired
0
0
0
0
Properly Paired(QC-failed)
0
0
0
0
% Properly Paired
0.0
0.0
0.0
0.0
With itself
0
0
0
0
With itself(QC-failed)
0
0
0
0
Singletons
0
0
0
0
Singletons(QC-failed)
0
0
0
0
% Singleton
0.0
0.0
0.0
0.0
Diff. Chroms
0
0
0
0
Diff. Chroms (QC-failed)
0
0
0
0
Marking duplicates (filtered BAMs)
rep1
rep2
ctl1
ctl2
Unpaired Reads
21674644
16282593
17088848
19256817
Paired Reads
0
0
0
0
Unmapped Reads
0
0
0
0
Unpaired Dupes
1123160
621651
2823373
821225
Paired Dupes
0
0
0
0
Paired Opt. Dupes
0
0
0
0
% Dupes/100
0.051819
0.038179
0.165217
0.042646
Filtered out (samtools view -F 1804):
read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)
Fraction of mitochondrial reads
rep1
rep2
ctl1
ctl2
Total reads
60127217
47393516
47463142
56139379
Mito. reads
155493
169103
172364
251409
Frac. of mito. reads
0.00258606680565
0.00356806192645
0.00363153370672
0.00447830033888
Total deduped reads
20551484
15660942
14265475
18435592
Mito. deduped reads
10862
10918
11099
11702
Frac. of deduped mito. reads
0.000528526309828
0.000697148357998
0.000778032277229
0.00063475043275
Total dup reads
1123160
621651
2823373
821225
Mito. dup reads
48335
49568
62642
81705
Frac. of mito. dup reads
0.0430348303002
0.0797360576915
0.0221869373972
0.0994916131389
SAMstat (filtered/deduped BAM)
rep1
rep2
ctl1
ctl2
Total
20551484
15660942
14265475
18435592
Total(QC-failed)
0
0
0
0
Dupes
0
0
0
0
Dupes(QC-failed)
0
0
0
0
Mapped
20551484
15660942
14265475
18435592
Mapped(QC-failed)
0
0
0
0
% Mapped
100.0
100.0
100.0
100.0
Paired
0
0
0
0
Paired(QC-failed)
0
0
0
0
Read1
0
0
0
0
Read1(QC-failed)
0
0
0
0
Read2
0
0
0
0
Read2(QC-failed)
0
0
0
0
Properly Paired
0
0
0
0
Properly Paired(QC-failed)
0
0
0
0
% Properly Paired
0.0
0.0
0.0
0.0
With itself
0
0
0
0
With itself(QC-failed)
0
0
0
0
Singletons
0
0
0
0
Singletons(QC-failed)
0
0
0
0
% Singleton
0.0
0.0
0.0
0.0
Diff. Chroms
0
0
0
0
Diff. Chroms (QC-failed)
0
0
0
0
Filtered and duplicates removed
Library complexity quality metrics
Library complexity (filtered non-mito BAM)
rep1
rep2
ctl1
ctl2
Total Reads (Pairs)
21615447
16222107
17015107
19163410
Distinct Reads (Pairs)
20542236
15651018
14258178
18424924
One Read (Pair)
19567078
15146483
11850474
17718375
Two Reads (Pairs)
902450
458775
2100982
682645
NRF = Distinct/Total
0.95035
0.964796
0.837972
0.961464
PBC1 = OnePair/Distinct
0.952529
0.967763
0.831135
0.961653
PBC2 = OnePair/TwoPair
21.682174
33.015057
5.640445
25.955475
Mitochondrial reads are filtered out by default.
The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads
in a dataset; it is the ratio between the number of positions in the genome
that uniquely mapped reads map to and the total number of uniquely mappable
reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations
with EXACTLY one read pair over the genomic locations with AT LEAST one read
pair. PBC1 is the primary measure, and the PBC1 should be close to 1.
Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking,
0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is
the ratio of genomic locations with EXACTLY one read pair over the genomic
locations with EXACTLY two read pairs. The PBC2 should be significantly
greater than 1.
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking
Alignment enrichment
Strand cross-correlation measures
rep1
rep2
Reads
15000000
15000000
Est. Fragment Len.
105
90
Corr. Est. Fragment Len.
0.207615704208
0.217655054133
Phantom Peak
35
35
Corr. Phantom Peak
0.2347065
0.2464728
Argmin. Corr.
1500
1500
Min. Corr.
0.1787521
0.1788231
NSC
1.161473
1.217153
RSC
0.5158422
0.574015
Performed on subsampled reads
NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.
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
