Stephen Turner

Bioinformatics template copyright notice

15

I used the Bioinformatics template to format a submission to a preprint server (biorXiv). The PDF was rejected because there's a copyright notice in the footer. Here's the email I...

contig IDs too long for Prokka

2

I'm getting the complaint: ``` [00:57:44] Contig ID must

Feature request: least common ancestor for equally scoring haplogroups

4

The feature released in 497cf6c13e23a7802eee5c3a96d07b855bff3119 in response to #12 allows for the export of the best _n_ haplogroups. When running with microarray data using the `--chip` flag, often there are...

As described in the README, the `--chip` flag will limit the range to array SNPs only. How are missing genotypes handled in a multisample VCF file? For example, my multisample...

update readme

1

need to update documentation with changes made in #6 by @aaronwolen to document automated creation of new datasets based on YAML files

better version/build management

3

with the changes in #6 it's much easier to recreate annotation tables. the files are named e.g. `galgal5`, but which version/build is actually used depends on what's current in ensembl....

do something with MSigDB

1

See http://bioinf.wehi.edu.au/software/MSigDB/ This could be useful in all sorts of ways.

a query with `-g "maf()>.10"` returns zero variants but `-g "maf()>0.10"` works.

In `formatVcfOutput` there is a line that adds "chr" to all chromosome names if there are any non-MT chromosomes without a "chr" prefix: https://github.com/Simon-Coetzee/motifBreakR/blob/098eeb8dfcf70b89ede1447814b2a6735cd2885e/R/locus.from.rsid.R#L132-L135 If I have a genome with...