MOSAIK not understanding ambiguity code in reference

[sktanz]

Hi Wan-Ping and Mosaik users,

I'm trying to use MOSAIK-2.2.3-Linux-x64 to align single end reads to a small reference genome, which contains ambiguity codes.

To test Mosaik first, I've aligned my reads to the reference genome (not containing any ambiguity code). I followed your QuickStart on github and used the following code:

Conversion (reference):
<MosaikBuild -fr ref.fa -oa ref.fa.dat>

Conversion (FASTQ):
<MosaikBuild -q read.fastq -st illumina -out reads.mkb>

<MosaikAligner -in reads.mkb -out reads.mka -ia ref.fa.dat -annpe 2.1.78.pe.ann -annse 2.1.78.se.ann -p 10>

This worked nicely for all my samples and 60-75% of my reads aligned, which is what I expected and also got with bowtie2.

Then I replaced all "C" in the reference to a "Y" (ambiguity code) so that reads containing a C or T at that position would also align. Repeating the alignment with this reference genome resulted that only 6-8% of reads aligned. However, I expected that more of my reads would map this time.

I'm not a bioinformatician and maybe I'm doing something wrong and/or need to add something to my command line?

Could you please help me to solve this problem?

Many thanks in advance,
Sandra

[alexstaj]

Did you solve this?

[sktanz]

No, I couldn't solve it, which is a real shame.