BWA, BOWTIE: what parameters for different analysis (ChIP, RNA, miRNA etc)

[dukevn]

Hi all,

I am still learning towards next generation sequencing and still do not have much experience on the field, so hopefully people are willing to share their experience. I wonder what parameters do people use (with BWA and/or BOWTIE) for different analysis such as ChIP-SEQ, RNA-SEQ, miRNA-SEQ etc... I read somewhere that mapping of data from RNA samples (RNAseq) presents different genome mapping challenges than those from DNA, that means there should be different parameters / options for different mapping analysis. Anybody has any advice?

Thanks,

D.

[mrawlins]

I asked a similar question (limited to RNA-Seq) on the Q/A site. The link to that and the answers is

http://i.seqanswers.com/question/198/optimal-parameters-for-bowtiebwa-on-solid

I found that using Bowtie for RNA-Seq we benefited from a larger error tolerance in the tail (-e 980) than we would have wanted for DNA. Mostly that's because we weren't particularly interested in SNP calling in those samples.

[dukevn]

I asked a similar question (limited to RNA-Seq) on the Q/A site. The link to that and the answers is

http://i.seqanswers.com/question/198/optimal-parameters-for-bowtiebwa-on-solid

I found that using Bowtie for RNA-Seq we benefited from a larger error tolerance in the tail (-e 980) than we would have wanted for DNA. Mostly that's because we weren't particularly interested in SNP calling in those samples.

Thanks for the link, mrawlins. Even it does not fully answer my question (parameters for ChIP vs RNA vs miRNA etc), and that it is for SOLID only, but it does give me some infos about parameter that others are using.

Thanks,

D.