Selected article for: "error rate and maximum error rate"
Author: Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy
Title: Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance
  • Document date: 2020_1_18
    • ID: bf4qpsy7_55
    Snippet: Read quality was assessed using FastQC. Adapters were trimmed from the 3' ends of reads using cutadapt 1.16 (Martin, 2013) with a maximum 10% error rate, minimum 2 bp overlap, and minimum 20 quality score. Each read contained a 6 bp UMI enabling PCR deduplication by collapsing UMIs followed by UMI trimming using PRINSEQ lite 0.20.2 (Schmieder and Edwards, 2011) . Processed reads with a minimum length of 15 bp were mapped to the hg38 genome modifi.....
    Document: Read quality was assessed using FastQC. Adapters were trimmed from the 3' ends of reads using cutadapt 1.16 (Martin, 2013) with a maximum 10% error rate, minimum 2 bp overlap, and minimum 20 quality score. Each read contained a 6 bp UMI enabling PCR deduplication by collapsing UMIs followed by UMI trimming using PRINSEQ lite 0.20.2 (Schmieder and Edwards, 2011) . Processed reads with a minimum length of 15 bp were mapped to the hg38 genome modified with the addition of a single copy of the human Pol I ribosomal RNA complete repeating unit (GenBank U13369.1) with BWA 0.7.13 (Li and Durbin, 2010) using the BWA-backtrack algorithm. Each read was represented by a single base at the 5' end of the read, corresponding to the 5' end of the nascent RNA. Data was converted to bigwig format using bedtools 2.27.1 (Quinlan and Hall, 2010) and UCSC bedGraphToBigWig v4 (Kent et al., 2010) for visualization and identification of TREs. Bigwig files from identical conditions were merged and normalized to a total signal of 1x10 6 prior to visualization.

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