Sample name: HelaS3_GRO-seq

Log file Pipeline profile Pipeline commands Stats summary file


Looper stats summary

sample_name HelaS3_GRO-seq
sample_desc HelaS3 GRO-seq
treatment none
replicate 1
toggle 1
protocol GRO
organism human
read_type SINGLE
cell_type HelaS3
purpose low pause index; high mRNA contamination; no adapter dist...
umi_status FALSE
umi_length 0
data_source SRA
read1 /project/shefflab/data/sra_fastq/SRR1693611.fastq.gz /pro...
srr SRR169361[1-2]
srx SRX796411
Sample_title HelaS3_GRO-seq
Sample_geo_accession GSM1558746
Sample_source_name_ch1 HelaS3_cells
Sample_characteristics_ch1 cell type: HelaS3
Sample_extract_protocol_ch1 For 5’GRO-seq, immunoprecipitated RNA was dephosphorylate...
Sample_description run-on RNA
Sample_data_processing Supplementary_files_format_and_content: bedGraph files ar...
Sample_platform_id GPL16791
Sample_contact_name Scott,Allen,Lacadie
Sample_contact_email [email protected]
Sample_contact_laboratory Ohler
Sample_contact_department Berlin Institute for Medical Systems Biology
Sample_contact_institute Max Delbrück Center for Molecular Medicine
Sample_contact_address Robert-Rössle-Str. 10
Sample_contact_city Berlin-Buch
Sample_contact_zip/postal_code 13092
Sample_contact_country Germany
Sample_instrument_model Illumina HiSeq 2500
Sample_library_selection cDNA
Sample_library_source transcriptomic
Sample_library_strategy RNA-Seq
Sample_relation SRA: https://www.ncbi.nlm.nih.gov/sra?term
gsm_id GSM1558746
Sample_supplementary_file_1 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1558nnn/GSM1558...
Sample_supplementary_file_2 ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1558nnn/GSM1558...
Sample_series_id GSE63872
File_mb 3550.33
Read_type single
Genome hg38
Raw_reads 72718941
Fastq_reads 72718941
Reads_with_adapter 22179715.0
Uninformative_adapter_reads 0.0
Pct_uninformative_adapter_reads 0.0
Trimmed_reads 72718941
Trim_loss_rate 0.0
Peak_adapter_insertion_size 0
Degradation_ratio 0.0
Aligned_reads_human_rDNA 40879756.0
Alignment_rate_human_rDNA 56.22
Mapped_reads 21029691
QC_filtered_reads 6163527
Aligned_reads 14866164
Alignment_rate 20.44
Total_efficiency 20.44
Read_depth 2.34
Mitochondrial_reads 1906316
Maximum_read_length 51
Genome_size 3099922541
NRF 0.72
PBC1 0.91
PBC2 13.55
Unmapped_reads 10809494
TSS_coding_score 7.3
TSS_non-coding_score 4.1
Pause_index 6.18
Plus_FRiP 0.37
Minus_FRiP 0.33
mRNA_contamination 3.22
Time 1:23:01
Success 02-27-10:47:33

HelaS3_GRO-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