I am working with Nanopore 16S amplicon data from individual microbial strains (1 strain sequenced per barcode) and I have little information about the prior processing of the data.
I noticed that when running fastplong v0.4.1 with the default adapter detection step that the detected adapter sequence was not an adapter but an actual part of the sequenced 16S sequence.
Command run: fastplong -i $file -l 1300 --length_limit 1600 --mean_qual 12 --cut_front 12 --thread 2 -o results/fastplong/indiv/${barcode}_filtered.fastq.gz
To still check/remove possible adapters I decided to instead provide a file with -a:
fastplong -i $file -l 1300 --length_limit 1600 --mean_qual 12 --cut_front 12 -a files/nanopore/all_sequences_unique.fasta -o results/fastplong/indiv/${barcode}_filtered.fastq.gz
Now slightly more bp are trimmed but the same incorrect part of the 16S sequence was returned as detected adapter. So if I understand this correctly the behavior now seems to be that there is still the automatic detection of sequences and additional check of the provided sequences in the fasta file.
My question is if I understand the behavior correctly and if so whether it is would possible to when providing a fasta file with adapters via -a to not run the automatic detection step if that is desired?
Thanks for considering.
I am working with Nanopore 16S amplicon data from individual microbial strains (1 strain sequenced per barcode) and I have little information about the prior processing of the data.
I noticed that when running fastplong v0.4.1 with the default adapter detection step that the detected adapter sequence was not an adapter but an actual part of the sequenced 16S sequence.
Command run:
fastplong -i $file -l 1300 --length_limit 1600 --mean_qual 12 --cut_front 12 --thread 2 -o results/fastplong/indiv/${barcode}_filtered.fastq.gzTo still check/remove possible adapters I decided to instead provide a file with -a:
fastplong -i $file -l 1300 --length_limit 1600 --mean_qual 12 --cut_front 12 -a files/nanopore/all_sequences_unique.fasta -o results/fastplong/indiv/${barcode}_filtered.fastq.gzNow slightly more bp are trimmed but the same incorrect part of the 16S sequence was returned as detected adapter. So if I understand this correctly the behavior now seems to be that there is still the automatic detection of sequences and additional check of the provided sequences in the fasta file.
My question is if I understand the behavior correctly and if so whether it is would possible to when providing a fasta file with adapters via -a to not run the automatic detection step if that is desired?
Thanks for considering.