Which software to use to map 100bp DNA sequence to genome

Question

[izzy.yichao.cai]

Hi all!

I have some fastq files of 100bp of DNA sequences(From a ChIP-seq experiment). Which software should I use to better map to genome?

In the original paper, the author used STAR to map. Is it suitable?

Or should I try Bowtie, Bowtie2 or Tophat? Can anyone tell me the length of read of each software so that I can have a better comparison on these software?

Thanks!

Answer 1

[Devon Ryan]

STAR is fine, as is bowtie2 (not tophat) or bwa, or bbmap, or ...

At the end of the day, just pick a popular aligner and become familiar with its parameters. 99% of the time they're fairly interchangeable for DNA alignment.

Answer 2

[predeus]

Every time I see someone using Tophat or suggesting using it (unless you're dealing with colorspace RNA-seq) I cringe a little :) Bwa does better job estimating mapping quality, which is pretty important for variant calling. Otherwise, any genomic aligner that's well supported would do equally well. Bowtie2 is fast and perfectly adequate for a ChIP-seq.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

Answer 3

[WouterDeCoster]

Tophat starts from 75bp, so the length is fine. But Tophat is optimized for spliced alignments, e.g. RNA-seq. As far as I know you don't expect introns in your ChIP-seq and therefore spliced alignments are definitely not what you want. I have no experience with STAR but I also believe it's for spliced alignments. Perhaps you can turn this off, but it's not it's purpose.

I would suggest to go with BWA. Just normal alignment for stuff like targeted resequencing or WES.

Answer 4

[chen]

Suggest you to use BWA mem