RNA-seq analysis

Question

[raavi21198]

I gave paired end fastq files for trimmomatic which gives me four output files. My doubt is when i give the files for alignment with Hisat tool, I should be giving both paired and unpaired output files of trimmomatic for alignment. Am I correct? Please let me know

Answer 1

[lieven.sterck]

Depends.

Nowadays (== with current accuracy etc of the sequencing) it should not happen you have much data in the unpaired files so you might consider to only continue with the true paired ones after trimming (that should as said be the vast majority of your input files). This is what most people will do I would think

In the unlikely case where there are a substantial amount of data in the unpaired files you could consider to use them as well. However, in this case I would personally double check of everything went OK in the trimming step.

[raavi21198]

Thank you for your input.