gold3


Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary
sample_name gold3
sample_description ATAC-seq from dendritic cell (ENCLB887PKE)
treatment_description Homo sapiens dendritic in vitro differentiated cells treated with 0 ng/mL Lipopolysaccharide for 0 hours
organism human
protocol ATAC-seq
data_source SRA
SRR SRR5210398
SRX SRX2523862
Sample_geo_accession GSM2471249
Sample_series_id GSE94177
read_type PAIRED
Sample_instrument_model Illumina NextSeq 500
read1 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210398_1.fastq.gz
read2 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210398_2.fastq.gz
File_mb 4809.4498
Read_type paired
Genome hg19
Raw_reads 166092252
Fastq_reads 166092252
Trimmed_reads 166090588
Trim_loss_rate 0.0
Aligned_reads_rCRSd_3k 29229450.0
Alignment_rate_rCRSd_3k 17.6
Aligned_reads_human_repeats 10699930.0
Alignment_rate_human_repeats 6.44
Mapped_reads 123357375
QC_filtered_reads 9669147.0
Aligned_reads 113688228
Alignment_rate 68.45
Total_efficiency 68.45
Mitochondrial_reads 15230.0
NRF 0.9
PBC1 0.95
PBC2 18.86
Unmapped_reads 2803833.0
Duplicate_reads 3118698
Dedup_aligned_reads 110569530.0
Dedup_alignment_rate 66.57
Dedup_total_efficiency 66.57
TSS_Score 10.5998173292
Peak_count 99691
FRiP 0.154924879294
Time 5:16:57
Success 01-03-19:50:48