Daniel Blankenberg

icon indicating a website link https://dblankenberg.org/

icon company Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic icon location Cleveland, OH, USA icon location Hiring postdocs and devs https://blankenberglab.org/jobs

Results 25 comments of Daniel Blankenberg

[WIP] Enhance cut tool

These are still useful abilities. Needs tests and conflicts resolved. I'll move the title into WIP.

Add mm10 to sicer

The biggest issue here has to do with the fact that sicer (`GenomeData.py`) itself needs to be modified to work with each new genome build. Apparently I wrote to the...

Data manager for the BLAST database *.loc files?

Hi all, this sounds great. Let me know what I can do to help. Thanks.

Data manager for the BLAST database *.loc files?

I have no objection to an MIT license. What ever is easier/more convenient for you. As far as paths are concerned, the `data_manager_blastdb` is just the repository root, with `data_manager`...

Data manager for the BLAST database *.loc files?

@peterjc Looks good to me. (But haven't had a chance to test it yet) @mike8115 e.g., A cron job could be set up to run a script against the API...

Data manager for the BLAST database *.loc files?

@jj-umn is correct. Data managers use namespacing on the .loc files that are installed from a toolshed, i.e. the entries created by the data manager tool will not end up...

Assemble a list of members

I am interested.

Custom reference genomes, bowtie fails to recognize

It looks OK, but it won't handle the case where you might have multiple different versions of indexes available for a dbkey (e.g. hg19cannonical vs hg19female).

Consistency with Rpy 1 and NumPy packages and tools, e.g. linear_regression

During a chat, @martenson also pointed out that an other good option is to move to conda only for any effected tools.

fastq groomer does not parse sequence ids that contain spaces properly

I suppose that the english is slightly off and the error could perhaps be more readable as `could not find quality score(s) for sequence identified as "@ ".`, as this...