Hi everyone,
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!
Thank you!
If you have
dos2unix
command available on your machine just pass yourinput.txt
file through it to ensure that line endings are proper.Thank you for the suggestion! I read through the material and will likely go that way.