Library | Type | Total (million) | BWA | Novoalign |
|---|
| Â | Â | Â |
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.
