Hello. I’m completely new to bioinformatics and I need to analyze some C. elegans paired-end whole genome sequencing data from illumina NovaSeq 6000. I’ve been reading and comparing multiple manuals for beginners, and I’ve come across MiModD’s manual “Mapping by sequencing: identification of a pheno…

Hi and welcome, fcy! You have done a good bit of reading, obviously, before asking here, but it looks like it is necessary to put a few things into perspective still. It is true that Bowtie2 and BWA-MEM are excellent aligners, just like FreeBayes is an excellent variant caller - not just for C.ele…

Thank you wm75! I’m looking for a homozygous phenotype causing mutation in my genomic DNA, induced by EMS and backcrossed to filter out background variations - so it’s a fairly simple and straightforward setup. You’re probably right about the small improvement gap between using the MiModD workflow…

[image] fcy: VCFAllelicPrimitives This tool is available at Galaxy Main https://usegalaxy.org . Search the tool panel with the full tool name to find it. The tool form describes what it does.

You don’t say whether you used freebayes to call the variants from all your samples together (the recommended approach) and now have 1 vcf, or whether you ran things separately and have 3 files now.

Thank you Jen, I’ll look it up!

I see. You should be able to use MiModD VCF Filter for simple variant subtraction then. You won’t be able to make use of all possible settings (because some VCF keys expected by MiModD will not exist in the freebayes-generated VCF), but filtering for genotypes (combined with depth of coverage) shoul…

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When does in-file metadata matter, and what tools on galaxy can help me do so?

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