peterdfields
peterdfields
Hi @singing-scientist I'm using SNPGenie on a number of poolseq samples. For at least some samples I am seeing estimates of mean_gdiv_polymorphic which are negative. Have you ever observed this...
Hi @ktrappe I don't think the present samtools (v. > 1.x) will work with the present scripts. More recent versions of samtools require specification of the output file name when...
Hi, I was just wondering if there are any updates regarding the release of the software version for python3 and tensorflow? Best regards
**1. What were you trying to do?** I would like to identify structural variant (SV) type (e.g., ``, ``, etc.) as part of the `vg call` step on a gam...
Hi, I'm trying to use MitoHiFi to assemble a multi-chromosome plant mitochondrial genome (though running the pipeline on individual chromosomes at a time). I'm using a singularity instance built from...
Hi, I'm trying to run the example commands and getting the following error: ``` ./pyScaf.py -f test/contigs.reduced.fa -r test/ref.fa -o test/contigs.reduced.ref.fa Options: Namespace(dotplot='png', fasta='test/contigs.reduced.fa', fastq=None, identity=0.33, joins=5, linkratio=0.7, load=0.2, log=,...
Continue to get a render error on this particular gene.
Hi, I'm trying to run AnchorWave on a pair of non-plant genomes. Whether I use minimap2 or gmap when I run the `anchorwave genoAli` function I see the following: ```...
I would like to compare SV calls between two different methodologies, for example between a graph-based method and one which uses only a single linear reference. Is it reasonable to...
Hi, I've noticed that for some datasets the TransPi (conda controlled) seems to sort of get stuck in the Trinity assembly phase. Basically the pipeline stays in the `salmon index`...