gjeunen
commented
2 months ago Hello @nroux66,
Thank you for using CRABS.
When we developed CRABS, the reference database for dada2 was split into two files, which are the format options of --format dad and --format dads. The --format dad option is the one you have right now and does not contain the species information. The --format dads option is a second database that contains the species information for each reference sequence. I believe you need both for dada2.
Please let me know if the formatting requirements for dada2 changed in newer versions of dada2, and we can alter the formatting of the CRABS output for dada2 so that it fits the formatting requirements of dada2.
I hope this helps.
Best wishes, Gert-Jan
nroux66
First thank you very much for all the detailed explanations provided to run your programm. It's really great, especially for people who are just beginning programming. I have successfully retrieved marine mammals sequences for a 16S marker, however I noticed that when running the tax_format function to save my database to be used in dada2 (using the format dad) I am loosing the species name in the process, keeping only the genus. Is it normal ? if not how could I solve this ? I double checked that all the taxonomic informations, included species name are in the input file used to run the command tax_format. Here is an example of the given file: OP205218 302098 Eukaryota Chordata Mammalia Artiodactyla Balaenidae Eubalaena Eubalaena_japonica DNA SEQUENCE
and here is what I get after running the following command on WSL:
Command used: docker run --rm -it \ -v $(pwd):/data \ --workdir="/data" \ quay.io/swordfish/crabs:0.1.7 \ crabs tax_format \ --input cetacea_16SMarver3_singlespFilt.tsv \ --output cetacea_16SMarver3_singlespFiltDADA2.fasta \ --format dad
Thank you very much for your help.