Mapping Chip-seq with BWA or Bowtie2?

[viv]

Hi,
I am new to next generation sequencing analysis. So I need to map my 8 ChIP-seq samples(transcription factor) and I don't want to use galaxy.
So I was wondering what will be differences whether I use bowtie2 or bwa? And what kind of parameters should I use for aligning my reads?

P.S: Out of curiosity and since our department has DNAstar license, I would be grateful if you tell me your views on mapping with DNAstar?

[Brian Bushnell]

Chip-seq reads are often very short. The choice of mapper can depend on the length of your reads, the platform, quality (error rate and type), and whether they are paired; some mappers do not really make good use of pairing information. Also, your experiment is important - whether the reference is exactly the same strain as the sample, for example. So, can you better describe your reads?

Regardless, I would probably still recommend BBMap, because in my tests it is more accurate than others. But I've never heard of DNAstar, so I have not included it in any of my comparative tests; therefore, it could be better than anything I've tested, though I consider that unlikely.

[viv]

So l'fe done sequencing in 50bp single end mode. And my samples are from human cell line...

[Brian Bushnell]

For single-end 50bp Chip-seq using a high-quality reference (such as human), any good mapper should be fine. But if by 'human cell line' you mean an immortalized human cancer cell line, that would of course be full of mutations, so you should map allowing low-identity matches. Is that the case?