I have 44 pairs of fastq files which I want to assembly using Trinity. I want to use the trinity output fasta file to map the contigs back to each fastq files to get the expression profiles (using bowtie) so I can do the differential analysis. The reason I want to do such a trinity assembly is because we don't have a good reference genome.
However I am facing a question: assemble these 44 pairs of fastq files in one trinity job maybe really resource challenging. My cluster doesn't have enough space for the temporary files generated during this process. So I am wondering if there is any alternative approach I can do?
Can I assemble each pair first and then assemble the 44 trinity output fasta? Would these two be identical? Please let me know. Thank you very much!