Contents
Which is the best alignment tool for ChIP seq?
Bowtie2 is a fast and accurate alignment tool that indexes the genome with an FM Index based on the Burrows-Wheeler Transform method to keep memory requirements low for the alignment process. Bowtie2 supports gapped, local and paired-end alignment modes and works best for reads that are at least 50 bp (shorter read lengths should use Bowtie1).
When to use FastQC in a NGS analysis?
After receiving the raw FASTQ files from the sequencing facility, the quality of the data should be explored, similar to other NGS analyses. We have explored the sequencing quality using the FastQC tool to ensure the quality of the data is good prior to moving on to alignment.
How does post filtering affect BWA peak calls?
Post-filtering this translates to a significantly higher number of mapped reads and results in a much larger number of peaks being called (30% increase). When we compare the peak calls generated from the different aligners, the bwa peak calls are a superset of those called from the Bowtie2 aligments.
Why are there multiple mapped reads in ChIP seq?
An important issue with ChIP-seq data concerns the inclusion of multiple mapped reads (reads mapped to multiple loci on the reference genome). Allowing for multiple mapped reads increases the number of usable reads and the sensitivity of peak detection; however, the number of false positives may also increase [1].
What’s the difference between bwa and ChIP seq?
We have explored the use of bwa for ChIP-seq analysis and found some differences. For bwa, the mapping rates are higher (~ 2%), with an equally similar increase in the number of duplicate mappings identified.
Which is the best alignment tool to use?
Bowtie2 supports gapped, local and paired-end alignment modes and works best for reads that are at least 50 bp (shorter read lengths should use Bowtie1). By default, Bowtie2 will perform a global end-to-end read alignment, which is best for quality-trimmed reads.