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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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RGI bwt: paired end VS single end. Which one is better? #175

Closed valei closed 11 months ago

valei commented 2 years ago

Hi, I ran RGI bwt in a metagenome sample in two different ways: 1) using as input R1 and R2 paired-end files; 2) using as input a concatenated file R1+R2 and so considering the sample as single-end. The results at both allele and gene level are fully different for a large number of genes/alleles found (about 30/40%). I wonder, why is there such a big difference? What is the most reilable way to run the tool?

raphenya commented 1 year ago

@valei, which commands did you use to concatenate the files?

github-actions[bot] commented 1 year ago

Issue is stale and will be closed in 7 days unless there is new activity

valei commented 1 year ago

I used simply cat command: cat sample_R1.fastq sample_R2.fastq > sample.fastq

raphenya commented 1 year ago

@valei the cat command appends the reads. If you run rgi bwt with -1 and -2 i.e paired reads option and run again with either R1 or R2 with only -1, you should get the same results. Look for current methods on how to effectively merge the R1 and R2 into single end reads.

raphenya commented 11 months ago

@valei see https://drive5.com/usearch/manual9.2/merge_pair.html and https://drive5.com/usearch/manual9.2/cmd_fastq_mergepairs.html

raphenya commented 11 months ago

@valei I did some analysis you can see at https://github.com/raphenya/read-merging. Long story short merging with cat produces lower hit rate.

@agmcarthur note.

Cheers.