Sample name: gold1

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name gold1
sample_description ATAC-seq from dendritic cell (ENCLB065VMV)
treatment_description Homo sapiens dendritic in vitro differentiated cells trea...
organism human
protocol ATAC-seq
data_source SRA
SRR SRR5210416
SRX SRX2523872
Sample_geo_accession GSM2471255
Sample_series_id GSE94182
read_type PAIRED
Sample_instrument_model Illumina HiSeq 2000
read1 /project/shefflab/data/sra_fastq//SRR5210416_1.fastq.gz
read2 /project/shefflab/data/sra_fastq//SRR5210416_2.fastq.gz
Raw_reads 137944752
Fastq_reads 137944752
Trimmed_reads 137924802
Trim_loss_rate 0.01
Mapped_reads 103770862
QC_filtered_reads 8341982
Aligned_reads 95428880
Alignment_rate 69.19
Total_efficiency 69.18
Mitochondrial_reads 14500
NRF 0.94
PBC1 0.97
PBC2 32.71
Unmapped_reads 3342300
Duplicate_reads 2001987
Dedup_aligned_reads 93426893.0
Dedup_alignment_rate 67.74
Dedup_total_efficiency 67.73
Read_length 76
Genome_size 3099922541
Frac_exp_unique_at_10M 0.9721
TSS_score 9.3
Peak_count 382788
File_mb 6493
Read_type PAIRED
Genome hg38
Aligned_reads_rCRSd 21049900.0
Alignment_rate_rCRSd 15.26
Aligned_reads_human_repeats 9761740.0
Alignment_rate_human_repeats 7.08
Time 0:16:56
Success 09-15-12:33:08

gold1 objects

Figures
Fig.0 Library complexity
Fig.1 TSS enrichment
Fig.2 Fragment distribution
Fig.3 cFRiF
Fig.4 FRiF