Mapping RNAseq reads on assembled transcripts and SNP detection

[safa]

Hi everyone,

I am planning to assemble RNAseq data for ten different genotypes altogether and I need to detect SNPs through them but I am confused about the process and the needed softwares. What I understand is to detect SNPs, I need to map the cleaned reads to the assembled transcripts but I am not sure what softwares can be used to map RNAseq reads on assembled transcripts, would it be TopHat or what? and then use SAMtools to detect SNPs or what? Put in mind that I don't have reference genome. Any suggestions, clarifications would be appreciated.

[Brian Bushnell]

For mapping reads to a transcriptome, you don't need a splice-aware aligner such as Tophat; you can use any aligner (I suggest BBMap ). Subsequently, you can call SNPs with samtools or GATK.

[safa]

Thanks Brian, the genotypes I work on are plants, do you think BBmap can work for plants or it is more designed for microbes. Also, would Bowtie does this job too and which is better?
Thanks.

[GenoMax]

BBMap is a general purpose NGS data aligner (the entire suite of programs can do many other things). BBMap will work with data from any organism and is likely going to be faster than most aligners out there

[safa]

Thanks GenoMax so much. Will take a look on the BBmap pipeline and try to figure out how it works.