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Example code
```
import pims
image = pims.bioformats.BioformatsReader(somefilename)
```
And error messages that spit out
```
UserWarning: loci_tools.jar not found, downloading
warn('loci…
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Dear Omeed,
When running MTAG on the GWAS results of two related traits (UKB data, phenotypic correlation 0.6), with sample overlap, I picked up some loci that were not significant in the GWAS. Ho…
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Is there a way to highlight significant loci in the trumpet plot instead of annotating them?
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Hello,
I recently ran Susie fine mapping using tensoQTL's susie.map function. There were several loci where when I looked at the Manhattan plots for the QTL, it seemed like they should have had so…
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Hello Emese,
Firstly thank you for creating this repository, it is a really nice simple-to-use set of functions for COI databases. I'd like to ask your opinion on using it for making databases for …
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I'm unsure if this is related to #70. I've moved job testing over to the HPC because testing on a single node without slurm does not parallelize jobs as desired (which I sort of expected - although i…
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When running 1c_generate_sequence_lists.R, the script is halted with the following error:
```
Error: object 'failed_loci' not found
Execution halted
```
In the script, it looks like the object i…
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I ran a reference aligned assembly in ipyrad v.0.9.68 with 150bp paired-end ddRAD data and got some partially overlapping loci returned as separate loci and SNPs on those loci are duplicated in the SN…
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Add link to Loci Jupyter Notebooks on the http://loci.cat/ landing page.
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Hello,
We use instead of the normal workflow from snpir STAR pass-2 and the GATK best practises to create a bamfile. You recommend to use bwa-mem to align to the normal human reference genome to get …