Hi all,
I'm working with a set of Illumina paired-end data and my reference genome is a non-model organism made up of only scaffolds and contigs at the moment.
My overall aim is to use the reference as a guide for assembly as well as SNP calling.
My first question is, should I do assembly first and use it for SNP calling, or are these two processes separate and independent?
For now, I've decided to work on the SNP calling part first, by mapping my sequence reads (using BWA) to the set of publicly available reference scaffold and contigs. But before that, I did a quality trim step which left me with paired and unpaired reads (single).
My second question is, how do I deal with the unpaired reads? Can I also use them for SNP calling and later merge my SNP results with the ones I obtain with paired reads?
Any help/suggestion is much appreciated.
Thanks!
I'm working with a set of Illumina paired-end data and my reference genome is a non-model organism made up of only scaffolds and contigs at the moment.
My overall aim is to use the reference as a guide for assembly as well as SNP calling.
My first question is, should I do assembly first and use it for SNP calling, or are these two processes separate and independent?
For now, I've decided to work on the SNP calling part first, by mapping my sequence reads (using BWA) to the set of publicly available reference scaffold and contigs. But before that, I did a quality trim step which left me with paired and unpaired reads (single).
My second question is, how do I deal with the unpaired reads? Can I also use them for SNP calling and later merge my SNP results with the ones I obtain with paired reads?
Any help/suggestion is much appreciated.
Thanks!
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