Sample name: Jurkat_ChRO-seq_2

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name Jurkat_ChRO-seq_2
sample_desc Jurkat ChRO-seq
treatment none
replicate 2
toggle 1
protocol PRO
organism human
read_type SINGLE
cell_type Jurkat
purpose intact library
umi_status true_6
umi_length 6
data_source SRA
read1 /project/shefflab/data/sra_fastq/SRR7616134.fastq.gz
srr SRR7616134
srx SRX4480701
Sample_title Jurkat chromatin run-on 2 [ChRO-seq]
Sample_geo_accession GSM3309957
Sample_source_name_ch1 Jurkat T-cells
Sample_characteristics_ch1 batch: 2
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 GSM3309957
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 1914.91
Read_type single
Genome hg38
Raw_reads 49841170
Fastq_reads 49841170
Trimmed_reads 48264585
Trim_loss_rate 3.16
Reads_with_adapter 42416468.0
Uninformative_adapter_reads 223715.0
Duplicate_reads 5764233.0
Pct_uninformative_adapter_reads 0.4489
Peak_adapter_insertion_size 39
Degradation_ratio 0.4899
Aligned_reads_human_rDNA 3950647.0
Alignment_rate_human_rDNA 8.19
Mapped_reads 41878067
QC_filtered_reads 7874013
Aligned_reads 34004054
Alignment_rate 70.45
Total_efficiency 68.22
Read_depth 4.27
Mitochondrial_reads 18250
Maximum_read_length 70
Genome_size 3099922541
Frac_exp_unique_at_10M 0.6458
NRF 0.53
PBC1 0.8
PBC2 8.39
Unmapped_reads 2435871
TSS_coding_score 68.4
TSS_non-coding_score 23.2
Pause_index 78.33
Plus_FRiP 0.36
Minus_FRiP 0.35
mRNA_contamination 1.2
Time 2:17:43
Success 02-27-11:42:46

Jurkat_ChRO-seq_2 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