Using a transcriptome from Trinity in Phyluce

Question

[luzglongoria]

Hi there,

I'm working with multiple RNA seq samples. These samples belong to bird blood infected with malaria parasites. The genome reference for the parasite species is not available. Most of my reads belong to bird and I'm not interesting on them...only parasite.

I have created one single de novo assembly through Trinity based exclusively on parasite reads. So, the assembly has only parasite contigs and that's why I do need to run the analyses with it.

I'm interesting on genetic variation of my parasite population through analyzing SNPs. After reading what Phyluce can do, I have some questions:

In phyluce...

1) Can I use my Trinity assembly for mapping? I do NOT have a .gff file or similar... 2) Can I made SNP analyses with 42 samples ? I know they are a lot, but maybe I need to do it by groups?

Any help is more than welcome.

[Pierre Lindenbaum]

The genome reference for the parasite species is not available.

can't you use any reference genome for .P falciparum ?

[luzglongoria]

I could but I will lose too much information. I have already done a differential expression analyzed using the transcriptome in Trinity and getting very interesting results. I'm afraid that If I use another reference I'll lose that info.