Bowtie2 and MapQ Calculation

[KyuzoSeq]

Hi

I'm going to ask about bowtie2's mapping quality calculation for ChIP-Seq data. For sequences which align multiple locations Bowtie2 gives the MAPQ 30. It says for multiple aligned sequences, mapq is not meaningful, so why it gives 30 for all? Other thing it gives 30 for completely aligned sequence and sequences which has indels too. What is that 30 and why?

I attached a png file about my ask.

[GenoMax]

http://biofinysics.blogspot.com.au/2014/05/how-does-bowtie2-assign-mapq-scores.html

Here is added discussion on biostars: https://www.biostars.org/p/110958/

[Gonza]

Chip-seq mappers

Hello Geno Max and all,

I am inquiring about Chip-seq mapping software. I am using the Arabidopsis TAIR10 genome as a reference.

I have used for RNA-seq tophat2 to account for splicing, which is something we are not really concerned when doing Chip-seq (right ?).

I have read that people uses Bowtie, and SOAP, SOAP2 when mapping against TAIR10. Before i get my Illumina reads, I'd like to know if you have an idea as to which mapper would be best?

Many thanks in advance.

Cheers

G

[GenoMax]

@Gonza: You could use any modern aligner for the alignment. You don't need to worry about splicing with ChIP-seq. I like @blancha's advice in a recent thread. Pick an aligner and become familiar with its myriad options (most have many) rather than hopping from one aligner to next.

[Gonza]

Hi GenoMax

I am mapping Illumina reads to a indexed genome with soap Version: 2.21 http://soap.genomics.org.cn/soapaligner.html

It seems to work fine, the only problem is that i cannot find the % of mapped reads. I am used to tophat that tells you % of mapped/unmapped. Is there a way to see % of mapped reads when using soap?

Script:
$soap -r 0 -M 1 -a sample1.fq -D genome.fa.index -o SOAP.sample1

Thanks

[GenoMax]

@Gonza: I am not familiar with soap but have you looked to see if soap writes any log files? Those may contain the information you are looking for.

Otherwise you could use "samtools idxstats" command or a package like Qualimap to find this information.

[Gonza]

thanks, will look into Qualimap