ASAP is a software from Babraham Bioinformatics Group that allows aligning NGS short reads to both parental genomes, a good reference can be found here.
The software can be downloaded here
A few things to keep in mind:
1. It only supports bowtie1, at least for now. Bowtie indexes for C3H and BL6 are located: /ddn/gs1/project/mousemeth/reference/C3H_NISC_Jan2012/Aug2012/indexBowtie/ /ddn/gs1/project/mousemeth/reference/BL6_NISC_Jan2012/Aug2012/indexBowtie/ 2. It needs to write output back to some directly where the raw files are stored, weird though Therefore, I had to make symbolic links: /ddn/gs1/home/li11/project2012/ASE/ASAP/filteredFastq/ 3. Here is a sample command: /ddn/gs1/home/li11/tools/ASAP/ASAP_v0.1.2/ASAP --solexa-quals -n 2 -l 40 --chunkmbs 8192 --genome_1 /ddn/gs1/project/mousemeth/reference/C3H_NISC_Jan2012/Aug2012/ --index_1 /ddn/gs1/project/mousemeth/reference/C3H_NISC_Jan2012/Aug2012/indexBowtie/NISC.C3H --genome_2 /ddn/gs1/project/mousemeth/reference/BL6_NISC_Jan2012/Aug2012/ --index_2 /ddn/gs1/project/mousemeth/reference/BL6_NISC_Jan2012/Aug2012/indexBowtie/NISC.BL6 /ddn/gs1/home/li11/project2012/ASE/ASAP/filteredFastq/C3_M_3.trimfilter.1.fastq /ddn/gs1/home/li11/project2012/ASE/ASAP/filteredFastq/C3_M_3.trimfilter.2.fastq
The problem is that no alignment was found at all!!
Let’s try a different way for alignment between mm9 and c3h. The command is here:
/ddn/gs1/home/li11/tools/ASAP/ASAP_v0.1.2/ASAP --solexa-quals -n 2 -l 40 --chunkmbs 8192 --genome_1 /ddn/gs1/project/mousemeth/reference/mm9/indexBowtie_mm9assembly/ --index_1 /ddn/gs1/project/mousemeth/reference/mm9/indexBowtie_mm9assembly/mm9 --genome_2 /ddn/gs1/project/mousemeth/reference/C3H_NISC_Jan2012/Aug2012/ --index_2 /ddn/gs1/project/mousemeth/reference/C3H_NISC_Jan2012/Aug2012/indexBowtie/NISC.C3H /ddn/gs1/home/li11/project2012/ASE/ASAP/filteredFastq/C3_M_3.trimfilter.1.fastq /ddn/gs1/home/li11/project2012/ASE/ASAP/filteredFastq/C3_M_3.trimfilter.2.fastq
