I’m trying to split my forward and reverse fastq files by sample for submission to SRA using an oligos file but all the sequences end up in the scrap files. I analyzed this data in v1.42.0 and have tried the command there as well as v1.43.0 and still no luck. When I ran make.contigs in the old version with the same exact files, the sequences worked just fine, so I’m kind of at a loss here.
fastq.info(file=2016File.file, oligos=2016Snook_Map.txt, checkorient=t, qfile=F, fasta=F)
I’ve included a link to my file, oligos, and original logfile (from the make.contigs I ran in the previous version).
Any help would be greatly appreciated!