I want to reconstruct phylogeny using RNA-seq data. I have downloaded the fasta file from SRA of NCBI. It contains paired reads (ILLUMINA HISEQ 2000). I want to construct the full transcriptome to put it as an input in MEGA for multiple sequence alignment.
What should I do now? Should I go for deNovo assembly (I have Downloaded fasta not fastq)? Should I use Galaxy server/Trinity etc.
Please suggest. Thanks.
Sincerely - Sunzid.