SamtoolsFlagstatsQualityMetric
DNase-seq, Total RNA-seq,
diff_chroms
flagstats: mate mapped different chr (mapQ>=5)
diff_chroms_qc_failed
flagstats: mate mapped different chr (mapQ>=5) - qc failed
duplicates
flagstats: duplicates
duplicates_qc_failed
flagstats: duplicates - qc failed
mapped
flagstats: mapped
mapped_pct
flagstats: mapped - percent
mapped_qc_failed
flagstats: mapped - qc failed
paired
flagstats: paired
paired_properly
flagstats: properly paired
paired_properly_pct
flagstats: properly paired - percent
paired_properly_qc_failed
flagstats: properly paired - qc failed
paired_qc_failed
flagstats: paired - qc failed
read1
flagstats: read1
read1_qc_failed
flagstats: read1 - qc failed
read2
flagstats: read2
read2_qc_failed
flagstats: read2 - qc failed
singletons
flagstats: singletons
singletons_pct
flagstats: singletons - percent
singletons_qc_failed
flagstats: singletons - qc failed
total
flagstats: total
total_qc_failed
flagstats: total - qc failed
with_itself
flagstats: with itself and mate mapped
with_itself_qc_failed
flagstats: with itself and mate mapped - qc failed
usable_fragments
Usable fragments, based on the mapped value.
SamtoolsStatsQualityMetric
DNase-seq, WGBS
1st fragments
samtools --stats: 1st fragments
average length
samtools --stats: average length
average quality
samtools --stats: average quality
bases duplicated
samtools --stats: bases duplicated
bases mapped
samtools --stats: bases mapped
bases mapped (cigar)
samtools --stats: bases mapped (cigar)
bases trimmed
samtools --stats: bases trimmed
error rate
samtools --stats: error rate
filtered sequences
samtools --stats: filtered sequences
insert size average
samtools --stats: insert size - average
insert size standard deviation
samtools --stats: insert size - standard deviation
inward oriented pairs
samtools --stats: inward oriented pairs
is sorted
samtools --stats: is sorted
last fragments
samtools --stats: last fragments
maximum length
samtools --stats: maximum length
mismatches
samtools --stats: mismatches
non-primary alignments
samtools --stats: non-primary alignments
outward oriented pairs
samtools --stats: outward oriented pairs
pairs on different chromosomes
samtools --stats: pairs on different chromosomes
pairs with other orientation
samtools --stats: pairs with other orientation
raw total sequences
samtools --stats: raw total sequences
reads MQ0
samtools --stats: reads MQ0
reads QC failed
samtools --stats: reads QC failed
reads duplicated
samtools --stats: reads duplicated
reads mapped
samtools --stats: reads mapped
reads mapped and paired
samtools --stats: reads mapped and paired
reads paired
samtools --stats: reads paired
reads properly paired
samtools --stats: reads properly paired
reads unmapped
samtools --stats: reads unmapped
sequences
samtools --stats: sequences
total length
samtools --stats: total length
CorrelationQualityMetric
Deprecated
Pearson correlation
Pearson's R correlation
Spearman correlation
Spearman's rank correlation
Items
Count of items from two different datasets that are being correlated
Standard deviation
Standard deviation of difference
MAD of log ratios
Mean-Average-Deviation (MAD) of replicate log ratios from quantification
Details
Description of methods