gold4


Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary
sample_name gold4
sample_description ATAC-seq from dendritic cell (ENCLB586KIS)
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 SRR5210428
SRX SRX2523884
Sample_geo_accession GSM2471269
Sample_series_id GSE94196
read_type PAIRED
Sample_instrument_model Illumina HiSeq 2000
read1 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210428_1.fastq.gz
read2 /sfs/lustre/allocations/shefflab/data/sra_fastq/SRR5210428_2.fastq.gz
File_mb 3135.7354
Read_type paired
Genome hg19
Raw_reads 101078490
Fastq_reads 101078490
Trimmed_reads 101077540
Trim_loss_rate 0.0
Aligned_reads_rCRSd_3k 14045392.0
Alignment_rate_rCRSd_3k 13.9
Aligned_reads_human_repeats 7514112.0
Alignment_rate_human_repeats 7.43
Mapped_reads 77776972
QC_filtered_reads 6666740.0
Aligned_reads 71110232
Alignment_rate 70.35
Total_efficiency 70.35
Mitochondrial_reads 6762.0
NRF 0.95
PBC1 0.97
PBC2 35.92
Unmapped_reads 1741064.0
Duplicate_reads 1017796
Dedup_aligned_reads 70092436.0
Dedup_alignment_rate 69.35
Dedup_total_efficiency 69.34
TSS_Score 7.47369732517
Peak_count 77891
FRiP 0.110209245274
Time 4:05:39
Success 01-03-18:40:00