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.

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