Trinity after trimmomatic

Question

[Princy]

Hello, I am new to Bioinformatics, I have done Trimmomatic of my fastq sequences, I have 4 samples with 3 replicates each. now I have paired and unpaired reads. Do I need to merge right and left paired read sequences? Please guide.

Answer 1

[andres.firrincieli]

Do I need to merge right and left paired read sequences?

No, you don't. Please, read the manual

[Princy]

I have paired and unpaired reads after trimmomatic. Do I only need to use paired reads for trinity? what should be the command for trinity for paired-end reads with replicates? do I need to add all left and right sequences with a comma in a single command? Trinity --seqType fq --max_memory 50G --left reads_1.fq --right reads_2.fq --CPU 6

[andres.firrincieli]

If you have multiple replicates would be advisable to use trinity with the --samples_file parameter; you can find a very nice tutorial here.

In regard to the unpaired reads, I do not have an straight answer for that because it seems that trinity does not have great support for using mixed single-end and paired-end data (link). If the unpaired reads are only a small fraction of the original library then I would not care too much about them, and move forward with a paired-end assembly (this is just my personal opinion)

[Princy]

Thank you for the tutorial.