Question: Unable to Visualize RGI results using JSON file upload
0
gravatar for zhangdengwei
4 months ago by
zhangdengwei50
zhangdengwei50 wrote:

Hi,

I took advantage of online CARD to visualize the JSON file generated by command-line RGI with metagenomic sequencing data, but I failed. Here is my code:

nohup rgi bwt --read_one ../../05.kneaddata/${i}/Clean_*_kneaddata_paired_1.fastq --read_two ../../05.kneaddata/${i}/Clean_*_kneaddata_paired_2.fastq --output_file ${i} --threads 8 --include_wildcard -a bowtie2 &

I finally got such error, as follows, whatever I opted for either DNA or protein sequence as the input type.

Whoops, looks like something went wrong.

Besides, the RGI cannot produce heat maps to display its result with metagenomic sequencing data? Are there any other good approaches to display my result?

Any suggestions would be appreciated. Thanks very much.

card metagenomics rgi • 136 views
ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 4 months ago by zhangdengwei50

RGI HEATMAP should help you solve this issue.

usage: rgi heatmap [-h] -i INPUT [-cat {drug_class,resistance_mechanism,gene_family}] [-f] [-o OUTPUT] [-clus {samples,genes,both}] [-d {plain,fill,text}] [--debug]

Creates a heatmap when given multiple RGI results.

optional arguments: -h, --help show this help message and exit -i INPUT, --input INPUT Directory containing the RGI .json files (REQUIRED) -cat {drug_class,resistance_mechanism,gene_family}, --category {drug_class,resistance_mechanism,gene_family} The option to organize resistance genes based on a category. -f, --frequency Represent samples based on resistance profile. -o OUTPUT, --output OUTPUT Name for the output EPS and PNG files. The number of files run will automatically be appended to the end of the file name. (default=RGI_heatmap) -clus {samples,genes,both}, --cluster {samples,genes,both} Option to use SciPy's hiearchical clustering algorithm to cluster rows (AMR genes) or columns (samples). -d {plain,fill,text}, --display {plain,fill,text} Specify display options for categories (deafult=plain). --debug debug mode

ADD REPLYlink written 3 months ago by Optimist90
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