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Table 2 BWA and Novoalign mapping of paired-end reads

From: HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

Library Type Total (million) BWA Novoalign
    A B C A B C
GSM850526 IP 8 86 5.09 8.91 92.71 4.75 2.54
GSM850528 Control 7.29 82.32 7.09 10.59 89.68 6.62 3.7
  1. The 45-bp paired-end ChIP-Seq data were from TF RUNX1. Raw reads were mapped to hg19 by both BWA and Novoalign. BWA parameters are: bwa aln -o 1 -l 32 -t 4 -k 2 and bwa sampe -n 10 -a 500 -o 10000 -N 10 -s. Novoalign parameters are: novoalign -i PE 250,30 -r Random --hdrhd off -c 1 -d reference.nix -F STDFQ -f end1.fastq end2.fastq -o SAM, where reference.nix is the reference sequence index file. A: percentage of pairs with at least one uniquely mapped end; B: percentage of pairs with multiple mapping locations; C: others, including unmapped pairs, pairs with only one mapped end and improperly mapped pairs with small insertion size or wrong orientation.