Sample name: K562_PRO-seq

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name K562_PRO-seq
sample_desc K562 PRO-seq
treatment none
replicate 1
toggle 1
protocol PRO
organism human
read_type SINGLE
cell_type K562
purpose gold standard
umi_status FALSE
umi_length 0
data_source SRA
read1 /project/shefflab/data/sra_fastq/SRR1554311.fastq.gz /pro...
srr SRR155431[1-2]
srx SRX683602
Sample_title K562 PRO-Seq
Sample_geo_accession GSM1480327
Sample_source_name_ch1 K562 cells
Sample_characteristics_ch1 pull-down substrate: streptavidin
Sample_extract_protocol_ch1 PRO-seq libraries were prepared as described previously (...
Sample_description This Sample represents two sequencing replicates.
Sample_data_processing Supplementary_files_format_and_content: Processed data fi...
Sample_platform_id GPL16791
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 2500
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 GSM1480327
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 38517.59
Read_type single
Genome hg38
Raw_reads 496581677
Fastq_reads 496581677
Reads_with_adapter 423059183.0
Uninformative_adapter_reads 12437983.0
Pct_uninformative_adapter_reads 2.5047
Trimmed_reads 484143694
Trim_loss_rate 2.5
Peak_adapter_insertion_size 34
Degradation_ratio 0.2312
Aligned_reads_human_rDNA 44680364.0
Alignment_rate_human_rDNA 9.23
Mapped_reads 434069790
QC_filtered_reads 46741044
Aligned_reads 387328746
Alignment_rate 80.0
Total_efficiency 78.0
Read_depth 29.61
Mitochondrial_reads 9149071
Maximum_read_length 100
Genome_size 3099922541
NRF 0.28
PBC1 0.54
PBC2 3.89
Unmapped_reads 5393540
TSS_coding_score 13.9
TSS_non-coding_score 5.8
Pause_index 10.8
Plus_FRiP 0.36
Minus_FRiP 0.34
mRNA_contamination 1.37
Time 13:05:37
Success 02-27-22:28:40

K562_PRO-seq objects

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