|
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
|
- 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.
