Sample name: K562_GRO-seq

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name K562_GRO-seq
sample_desc K562 GRO-seq
treatment none
replicate 1
toggle 1
protocol GRO
organism human
read_type SINGLE
cell_type K562
purpose degraded library; low pause index
umi_status FALSE
umi_length 0
data_source SRA
read1 /project/shefflab/data/sra_fastq/SRR1552484.fastq.gz
srr SRR1552484
srx SRX682020
Sample_title K562 GRO-seq
Sample_geo_accession GSM1480325
Sample_source_name_ch1 K562 cells
Sample_characteristics_ch1 antibody: anti-BrU (Santa Cruz Biotechnology, sc-32323-ac...
Sample_extract_protocol_ch1 GRO-seq libraries were prepared as in Core et al. (Core, ...
Sample_description cDNA (from nascent RNA)
Sample_data_processing Supplementary_files_format_and_content: Processed data fi...
Sample_platform_id GPL11154
Sample_contact_name Leighton,James,Core
Sample_contact_email [email protected]
Sample_contact_laboratory John T. Lis
Sample_contact_department Moleular Biology and Genetics
Sample_contact_institute Cornell University
Sample_contact_address 417 Biotechnology Building
Sample_contact_city Ithaca
Sample_contact_zip/postal_code 14853
Sample_contact_country USA
Sample_instrument_model Illumina HiSeq 2000
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 GSM1480325
Sample_supplementary_file_1 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1480nnn/GSM1480...
Sample_supplementary_file_2 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1480nnn/GSM1480...
Sample_series_id GSE60456
File_mb 1322.25
Read_type single
Genome hg38
Raw_reads 30363736
Fastq_reads 30363736
Reads_with_adapter 22296806.0
Uninformative_adapter_reads 1041369.0
Pct_uninformative_adapter_reads 3.4296
Trimmed_reads 29322367
Trim_loss_rate 3.43
Peak_adapter_insertion_size 22
Degradation_ratio 0.7189
Aligned_reads_human_rDNA 4309471.0
Alignment_rate_human_rDNA 14.7
Mapped_reads 22899670
QC_filtered_reads 4468262
Aligned_reads 18431408
Alignment_rate 62.86
Total_efficiency 60.7
Read_depth 2.65
Mitochondrial_reads 843399
Maximum_read_length 50
Genome_size 3099922541
NRF 0.7
PBC1 0.86
PBC2 8.69
Unmapped_reads 2113226
TSS_coding_score 23.9
TSS_non-coding_score 8.6
Pause_index 14.58
Plus_FRiP 0.34
Minus_FRiP 0.32
mRNA_contamination 1.33
Time 1:03:44
Success 02-27-10:28:17

K562_GRO-seq objects

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