I have 13 RNA seq datasets (demultiplexed fastq files) and I am trying to co-assemble them into contigs that are at least 1000 kb long and eventually perform a differential transcriptome analysis.
For start, I did a quality check with "illumina-utils" package and merged the reads with zero mismatch. Now I need to co-assemble them and obtain Contig files, fro which I've been advised to use Megahit.
Based on the Megahit tutorials, the input for co-assembly is supposed to be R1.fastq and R2.fastq, i.e. paired-end fastq files from different samples. However, what I have now (after the quality filtering and merging the overlapping pairs) is a bunch of *MERGED files for each sample.
I was wondering if Megahit can still be used for co-assembling already-merged reads or does it have to be pair-end files.
I'm quite new and crawling in the complex world of bioinformatics so any help/advice would be much appreciated.And please let me know if my question is not clear enough.