Question: Which software to use to map 100bp DNA sequence to genome
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gravatar for izzy.yichao.cai
3.0 years ago by
izzy.yichao.cai140 wrote:

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 • 1.1k views
ADD COMMENTlink modified 9 months ago by predeus860 • written 3.0 years ago by izzy.yichao.cai140
1
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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.

ADD COMMENTlink written 3.0 years ago by Devon Ryan88k
1
gravatar for predeus
9 months ago by
predeus860
Russia
predeus860 wrote:

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.

ADD COMMENTlink modified 9 months ago • written 9 months ago by predeus860
0
gravatar for WouterDeCoster
3.0 years ago by
Belgium
WouterDeCoster37k wrote:

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.

ADD COMMENTlink written 3.0 years ago by WouterDeCoster37k
0
gravatar for chen
3.0 years ago by
chen1.8k
OpenGene
chen1.8k wrote:

Suggest you to use BWA mem

ADD COMMENTlink written 3.0 years ago by chen1.8k
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