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Hi Alex,
Thanks for making the ORF-RATE pipeline public and accessible.
When running prune_transcripts.py with the following parameters in Python 2.7.15:
`prune_transcripts.py --inbed annot.b…
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### Contact Details
d.m.soanes@exeter.ac.uk
### What happened?
Microarray data was not cell sorted (small test dataset)
The first part of the QC pipeline seemed to work fine:
1: Column names were…
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I am trying to filter my Xenium data based on the quality values (QV) of the transcripts using "ReadXenium" and "mols.qv.threshold". However, if I filter with 2 different QV (e.g. high and low), the g…
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I am trying to run the pipeline on some targeted amplicon sequencing by using the recommended settings (by using eval as target eval and providing a .bed file).
The pipeline runs fine if I use
sn…
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# Description
It has been observed that manual segmentations of SC in MP2RAGE datas (`basel-mp2rage` `marseille-3T-mp2rage`) have some issues like:
- #266
- SC masks does not cover the entire…
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Currently the SWIR metadata doesn't have an obvious option for describing manual changes to the focus setting. The json metadata files have the following descriptors related to focus:
optics foca…
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**Create a global parameters list**
Terminology between pipelines and shared assets can differ. To help preserve shared content and familiarity between pipelines, subworkflows and modules, it would…
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In Issue https://github.com/biolink/ontobio/issues/341 we made a script for producing `enables o has_part -> enables` annotations in ontobio. We ran the results in a specialized jenkins job and posted…
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Hi @mattcieslak,
I pulled `0.19.0` and am testing it. SynthSeg is still crashing as it was in #598. A quick check of the error file suggests that the threads are still inheriting --omp-nthreads (se…
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For integration with Binder, `batch_processing.sh` should be converted into a Jupyter notebook. A few things to keep in mind while doing that:
- `dcm2niix` will be to be called as system UNIX call
-…