Question: Hisat2 or Bowtie2 for ChIP-Seq Data?
0
gravatar for hkarakurt
2.4 years ago by
hkarakurt100
hkarakurt100 wrote:

Hello everyone, I am analyzing a ChIP-Seq data and I aligned them with Bowtie2 with default parameters. I used to use Hisat2 for my RNA-Seq data but I heard Bowtie2 gives better results with short reads. Actually a friend said that

I have done the alignment step but I need to be sure.

Is Bowtie2 better than Hisat2 with ChIP-Seq data? Do default parameters give bad results?

Thank you.

sequencing chip-seq alignment • 2.4k views
ADD COMMENTlink modified 2.4 years ago by EagleEye6.7k • written 2.4 years ago by hkarakurt100
3
gravatar for EagleEye
2.4 years ago by
EagleEye6.7k
Sweden
EagleEye6.7k wrote:
  • HISAT2/STAR/Tophat: suitable for transcriptome based or RNA-seq alignment (splice-aware aligner)

  • Bowtie/Bowtie2/bwa: suitable for genome based alignment (ChIP-seq/WGS)

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by EagleEye6.7k

"HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)."

ADD REPLYlink written 24 months ago by mollitz70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 992 users visited in the last hour