ATAC-Seq QC Reports
MultiQC reports for Igor's ATAC-Seq proof-of-concept project.
- Sequenced by
- GSAF
- Job
- JA17277
- Run
- SA17121
- Setup
- 2x150
Report generated on 2017-10-17, 22:34 based on data in:
/scratch/01063/abattenh/byteclub/multiqc
General Statistics
Showing 6/6 rows and 5/7 columns.Sample Name | % Dups | % GC | M Seqs | M Reads Mapped | % Dups |
---|---|---|---|---|---|
50knuclei_S56_L007_R1_001 | 55.8% | 46% | 10.2 | ||
50knuclei_S56_L007_R2_001 | 54.7% | 46% | 10.2 | ||
5knuclei_S77_L008_R1_001 | 71.4% | 47% | 36.9 | ||
5knuclei_S77_L008_R2_001 | 68.5% | 47% | 36.9 | ||
brain_50k_nuclei | 18.3 | 15.3% | |||
brain_5k_nuclei | 57.3 | 43.6% |
FastQC
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
Sequence Quality Histograms
The mean quality value across each base position in the read. See the FastQC help.
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
Per Base N Content
The percentage of base calls at each position for which an N was called. See the FastQC help.
Sequence Length Distribution
Sequence Duplication Levels
The relative level of duplication found for every sequence. See the FastQC help.
Overrepresented sequences
The total amount of overrepresented sequences found in each library. See the FastQC help for further information.
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.
Samtools Flagstat
This module parses the output from samtools flagstat
. All numbers in millions.
XY counts
Mapped reads per contig
The samtools idxstats
tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.
Picard
Picard is a set of Java command line tools for manipulating high-throughput sequencing data.
Mark Duplicates
Bowtie2 insert size
Bowtie2 insert size distribution for alignments (bowtie2 --local -X2000 --no-mixed --no-discordant)
Mapping quality
Mapping quality distribution for aligned reads before filtering
Genome coverage
Genome coverage of mapped inserts (bedtools genomecov -fs), grouped into coverage count catgories