I am attempting to use FastUniq to remove PCR duplicates from my trimmed and paired sequencing reads (150 BP PE done on the Illumina HiSeq X).
I first created an input file:
ls site1_R1_P.fq site1_R2_P.fq > site1_input.txt
Everything looks fine:
$ cat site1_input.txt site1_R1_P.fq site1_R2_P.fq
But I am getting the error: "Error in open left fastq file site1_R1_P_qtrim.fq for read!"
I searched through the previous questions that relate to this error but the resolutions to those don't seem to apply - ex. misplaced spaces in the input.txt file (made sure there is no spaces), unusual symbols (tried running without any underscores in case that counted as "unusual").
At a bit of a loss and I bet it's something silly so I appreciate any help!