Guillaume Poirier-Morency

icon indicating a website link https://arteymix.github.io/about icon indicating an email [email protected]

icon company The University of British Columbia icon location Vancouver icon location Bioinformatics Programmer/Analyst at @PavlidisLab

Results 345 issues of Guillaume Poirier-Morency

Trimmed FASTQs are not deleted when data is successfully submitted to Gemma

For some reason, the `TrimExperiment` task returns nothing.

bug

Build and install the shared memory cleanup tool during initial setup

1 comment

Adjust FastQC limits to be suitable for RNA-Seq

1 comment

We can get an idea of the thresholds to apply by looking at the data we gathered so far.

Add BGI-SEQ adapters to the FastQC report

SRA prefetch fails with large downloads

The real issue is that the tool does not exit with a non-zero code when it fails due to a download size limit.

bug

Add support for Ion Torrent Proton platform

Add automated quality control checks before submitting data to Gemma

As per https://github.com/PavlidisLab/GemmaCuration/issues/3#issuecomment-759691608, it would be valuable to perform some sanity checks before submitting data to Gemma. Here's a list of basic things that we can do: - [ ]...

enhancement

Adapt the Web viewer for other data sources

enhancement

Only consider the relevant subset of samples when assessing batch info

enhancement

Support extracting batch information from FASTQ headers with underscores

I've encountered a couple of archives in SRA that replaces `:` separator by `_` in their FASTQ headers. We would have to handle this specific case in `ExtractGeoSeriesBatchInfo`.

enhancement