using more than one set of paired-end read files to run GetOrganelle

[Oscar Alejandro Perez Escobar]

Dear GetOrganelle team,

I have a two sets of paired end read files for a series of samples and I am wondering if there is any way to run GetOrganelle using as input multiple paired-end read files? For example, would the argument "-1 Sample1_ABC_R1.fq,Sample1_DEF_R1.fq -2 Sample1_ABC_R2.fq,Sample1_DEF_R2.fq" be valid? 
My read files are huge (these are produced from old herbarium specimens) and I am intending to use them all to retrieve complete or partial plastid and nuclear genomic regions. 

Also, any advice on how to optimise the analysis for degraded or contaminated samples is most welcome (I am open to consider a collaboration in this project!).

Best wishes,

Oscar

[JianJun Jin]

Hi Oscar,

Thanks for reaching out. Currently (GetOrganelle 1.7.7.1~1.8.0), you can use -1 Sample1_ABC_R1 -2 Sample1_ABC_R2 -u Sample1_DEF_R1.fq,Sample1_DEF_R2.fq. For most samples, using the first pair as a pair and the rest as unpaired like this, is generally good enough.

For genome assembly using short reads, more is not better. For organelle genomes, GetOrganelle will estimate the no. reads to use by estimating the target coverage and limiting it to be smaller than a bound (default: 500). You may change the value by using `--reduce-reads-for-coverage`.

For nuclear genomic regions, please see https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#how-to-assemble-custom-loci and https://github.com/Kinggerm/GetOrganelle/discussions/309.

Hope this helps.

JianJun

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