Which software to use to map 100bp DNA sequence to genome
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5.7 years ago

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!

ChIP-Seq • 1.6k views
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5.7 years ago

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.

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3.5 years ago
predeus ★ 1.7k

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.

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5.7 years ago

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.

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5.7 years ago
chen ★ 2.3k

Suggest you to use BWA mem

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