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BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
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Using CONCOCT to determine coverage of specific predicted ORFs in multiple samples #270

Closed slvrshot closed 4 years ago

slvrshot commented 4 years ago

I ran across this software when I was researching the map-bowtie2-markduplicates.sh tool described in https://buildmedia.readthedocs.org/media/pdf/metagenomics-workshop/2014-5/metagenomics-workshop.pdf file. I have some nucleotide sequences of predicted ORFs from prodigal and would like to determine the read coverage for these genes for each one of my samples (total of 28, divided into 4 groups). I have mapped my reads to the ORFs using bowtie2 and produced multiple sam files for each sample. Ultimately, I'd like to merge these datasets an create an ORF coverage matrix. Would CONCOCT be the right tool for this?

alneberg commented 4 years ago

Hi @slvrshot, there are many ways of accomplishing this. CONCOCT is not designed for this task specifically and I will have to refer you on to any these biostars questions: https://www.biostars.org/p/5165/ https://www.biostars.org/p/201722/

I hope you find what you're looking for there.