Sample name: Jurkat_ChRO-seq_1

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name Jurkat_ChRO-seq_1
sample_desc Jurkat ChRO-seq
treatment none
replicate 1
toggle 1
protocol PRO
organism human
read_type SINGLE
cell_type Jurkat
purpose degraded library
umi_status true_6
umi_length 6
data_source SRA
read1 /project/shefflab/data/sra_fastq/SRR7616133.fastq.gz
srr SRR7616133
srx SRX4480700
Sample_title Jurkat chromatin run-on 1 [ChRO-seq]
Sample_geo_accession GSM3309956
Sample_source_name_ch1 Jurkat T-cells
Sample_characteristics_ch1 batch: 1
Sample_extract_protocol_ch1 We prepared PRO-seq libraries as described in Kwak et. al...
Sample_description Jurkat chromatin run-on
Sample_data_processing Supplementary_files_format_and_content: *bw: Mapped reads...
Sample_platform_id GPL18573
Sample_contact_name Charles,G,Danko
Sample_contact_email [email protected]
Sample_contact_laboratory Danko Lab
Sample_contact_department Baker Institute
Sample_contact_institute Cornell University
Sample_contact_address Hungerford Hill Rd
Sample_contact_city Ithaca
Sample_contact_zip/postal_code 14853
Sample_contact_country USA
Sample_instrument_model Illumina NextSeq 500
Sample_library_selection other
Sample_library_source transcriptomic
Sample_library_strategy OTHER
Sample_relation SRA: https://www.ncbi.nlm.nih.gov/sra?term
gsm_id GSM3309956
Sample_supplementary_file_1 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3309nnn/GSM3309...
Sample_supplementary_file_2 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3309nnn/GSM3309...
Sample_series_id GSE117832
File_mb 1330.25
Read_type single
Genome hg38
Raw_reads 37740511
Fastq_reads 37740511
Trimmed_reads 32783879
Trim_loss_rate 13.13
Reads_with_adapter 34473620.0
Uninformative_adapter_reads 2012355.0
Duplicate_reads 14846147.0
Pct_uninformative_adapter_reads 5.3321
Peak_adapter_insertion_size 20
Degradation_ratio 0.9566
Aligned_reads_human_rDNA 3493243.0
Alignment_rate_human_rDNA 10.66
Mapped_reads 28177350
QC_filtered_reads 6839271
Aligned_reads 21338079
Alignment_rate 65.09
Total_efficiency 56.54
Read_depth 3.87
Mitochondrial_reads 4738
Maximum_read_length 70
Genome_size 3099922541
Frac_exp_unique_at_10M 0.7897
NRF 0.38
PBC1 0.64
PBC2 3.39
Unmapped_reads 1113286
TSS_coding_score 55.1
TSS_non-coding_score 12.6
Pause_index 50.36
Plus_FRiP 0.36
Minus_FRiP 0.34
mRNA_contamination 1.19
Time 1:26:16
Success 02-27-10:51:19

Jurkat_ChRO-seq_1 objects

Links
Figures
Fig.0 Adapter insertion distribution
Fig.1 Library complexity
Fig.2 TSS enrichment
Fig.3 Pause index
Fig.4 cFRiF
Fig.5 FRiF
Fig.6 mRNA contamination