Michael Heskett

Hey thanks for the response @LeilyR . skipNAs wont help since i need all files across samples to have the same set of regions. Is there any way to force...

Yeah you need to use bedtools intersect with sliding windows instead (see bedtools make windows) On Sat, Jul 9, 2022 at 8:34 AM Aannaw ***@***.***> wrote: > Hey, > Have...

Sorry I don't mean to pester, but I am just adding a vote for non-human species mainly mouse.

I got it to work kinda. Would be awesome if the creator added legitimate support for mouse, but i was able to hack it together if you want to email...

Rscript /home/groups/Spellmandata/heskett/english/ichorCNA/scripts/runIchorCNA.R --id $filename \ --WIG $sample_wig --gcWig ../mm10.reference/refdata-gex-mm10-2020-A/fasta/genome.gc.wig \ --chrs "c(\"chr1\",\"chr2\",\"chr3\",\"chr4\",\"chr5\",\"chr6\",\"chr7\",\"chr8\",\"chr9\",\"chr10\",\"chr11\",\"chr12\",\"chr13\",\"chr14\",\"chr15\",\"chr16\",\"chr17\",\"chr18\",\"chr19\",\"chrX\",\"chrY\")" \ --chrNormalize "c(\"chr1\",\"chr2\",\"chr3\",\"chr4\",\"chr5\",\"chr6\",\"chr7\",\"chr8\",\"chr9\",\"chr10\",\"chr11\",\"chr12\",\"chr13\",\"chr14\",\"chr15\",\"chr16\",\"chr17\",\"chr18\",\"chr19\",\"chrX\",\"chrY\")" \ --mapWig ../mm10.reference/refdata-gex-mm10-2020-A/fasta/genome2.50000.window.wig \ --ploidy "c(2)" --normal "c(0.9)" --maxCN 8 --includeHOMD False --estimateNormal True --estimatePloidy...

Excellent. You may want to see if they will put this guide into the main GitHub page instead of in an issue here On Mon, Aug 29, 2022 at 7:06...

> So a small help for those, who still want to do this with other genomes. First of all, many thanks for [Michael Heskett](https://github.com/mheskett)'s help with this! > > 1....

Thanks! @gavinha could you be more specific or include some commands? it would be a great help to just have a little example script where I can plug in my...

OK @gavinha i think this is something that should be included. I tried making mouse reference files myself and now im getting tons of errors because you hard coded the...

excellent! thank you On Tue, Feb 12, 2019 at 7:11 AM Dario Beraldi wrote: > If still interested, snp-pileup is now in bioconda > https://bioconda.github.io/recipes/snp-pileup/README.html > > — > You...