nomatch=keep is not working: still runs remove.seqs to separate the pcr.scraps from the .fasta and .count_table files.
Re-combining the fasta files is trickier than you might think, and requires going back to the start of the pipeline and using tools like awk or sed to keep trimming the sequence names to keep them matched to the earlier count_tables.
See attached output snippet that should explain things (also some weirdness in the number of sequences being screened by pcr.seqs which I ignored because once I was able to re-combine the trim and scraps and re-match them to the earlier count_table all was good.
Also just a note to say that this is my first foray into ITS sequences for a colleague who was banging her head against all the existing tools, and I was like "mothur is the most transparent and powerful tool I know, I bet I can make it work" and sure enough all the tools needed were there. So thank you to Pat, Sarah and Kendra for supporting my career for nearly two decades and remaining my favorite bioinformatics guideposts ;)
pcr.seqs.nomatch.example.txt
nomatch=keep is not working: still runs remove.seqs to separate the pcr.scraps from the .fasta and .count_table files.
Re-combining the fasta files is trickier than you might think, and requires going back to the start of the pipeline and using tools like awk or sed to keep trimming the sequence names to keep them matched to the earlier count_tables.
See attached output snippet that should explain things (also some weirdness in the number of sequences being screened by pcr.seqs which I ignored because once I was able to re-combine the trim and scraps and re-match them to the earlier count_table all was good.
Also just a note to say that this is my first foray into ITS sequences for a colleague who was banging her head against all the existing tools, and I was like "mothur is the most transparent and powerful tool I know, I bet I can make it work" and sure enough all the tools needed were there. So thank you to Pat, Sarah and Kendra for supporting my career for nearly two decades and remaining my favorite bioinformatics guideposts ;)
pcr.seqs.nomatch.example.txt