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xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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Calculated abundance for paired-end sequencing #57

Open JingliangShi opened 4 months ago

JingliangShi commented 4 months ago

In ARGs-OAP V3.2, each sample produces paired-end files corresponding to two results of ARGs abundance. I wonder if the abundance of ARGs from each sample is the sum of the abundances of the paired-end files. Thank you for your reply.

xinehc commented 4 months ago

if your paired files ends with _1|_2, _R1|_R2 or _fwd|_rev, a sample should show up only once in your output file.

if the abundance is defined as copies per 16s/cell/Gb, then you cannot simply sum the abundance of _1 and _2 up.

JingliangShi commented 4 months ago

if your paired files ends with _1|_2, _R1|_R2 or _fwd|_rev, a sample should show up only once in your output file.

if the abundance is defined as copies per 16s/cell/Gb, then you cannot simply sum the abundance of _1 and _2 up.

Thanks for your answer! Can we calculate the average value of them as the relative abundance (copies per 16s/cell/Gb)?

xinehc commented 4 months ago

yes, _1 and _2 should have similar abundance