I am new to RNAseq and have just started working with HISAT2. Using trimmomatic I QCed an illumina paired end run and got 4 files: paired1.fq, paired2.fq were my paired reads after QC and unpaired1.fq, unpaired2.fq were files containing unpaired reads (presumably their partners didn't make the cut).
I went to run HISAT2 for the first time and tried to use the following commandline:
hisat2 -x genome_snp_tran -1 paired1.fq,-2 paired2.fq -U unpaired1.fq,unpaired2.fq -S test_output
only to get the following error:
Extra parameter(s) specified: "trimmed2paired.fastq" Error: Encountered internal HISAT2 exception (#1)
This problem is solved by deleting one set of reads (either the paired or unpaired files) at which point the program starts running. Can I take it from this that Hisat2 can only work with one type of data at a time? If so what is the best way to deal with my unpaired read file? Should I simply treat all the QCed reads as SE data and run it in unpaired mode? Or should I try to produce output for both the paired and unpaired files separately then combine the output somehow later? Or is there a way to use both paired and unpaired reads simultaneously with a correctly worded commandline. Is so could you provide an example?
Any help you could provide in this matter would be greatly appreciated!