AlexsLemonade / AlexsLemonade/refinebio
Support RNA-Seq experiments with more than one organism
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
### Context
We've processed only 394 of 54788 RNA-Seq samples that belong to experiments with two organisms:
```
data_refinery=> select sum(num_total_samples) as total_sum, sum(num_processed_samples) as processed_sum from experiments where id in (select filtered_exps.id from (select experiments.id, count(experiment_organism_associations.organism_id) from experiments full join experiment_organism_associations on experiments.id=experiment_organism_associations.experiment_id where experiments.technology='RNA-SEQ' group by experiments.id having count(experiment_organism_associations.organism_id)=2) as filtered_exps);
total_sum | processed_sum
-----------+---------------
54788 | 394
```
There's another 20k unprocessed samples if we consider experiments with even more than 2 organisms:
```
data_refinery=> select sum(num_total_samples) as total_sum, sum(num_processed_samples) as processed_sum from experiments where id in (select filtered_exps.id from (select experiments.id, count(experiment_organism_associations.organism_id) from experiments full join experiment_organism_associations on experiments.id=experiment_organism_associations.experiment_id where experiments.technology='RNA-SEQ' group by experiments.id having count(experiment_organism_associations.organism_id)>2) as filtered_exps);
total_sum | processed_sum
-----------+---------------
20856 | 38
```
although we may want to be careful because at the high end of the spectrum https://www.refine.bio/experiments/SRP042651/comparative-population-genomics-in-76-metazoan-species-popphyl-project has 76 different organisms.
### Problem or idea
My assumption is that at least some of these experiments are failing because tximport is not expecting to be given quant files from multiple organisms.
### Solution or next step
Change the `run_tximport_for_experiment()` function of the salmon processor to handle multiple organisms. This will probably require invoking tximport once per organism, however @jaclyn-taroni should probably weigh in on if this is actually a good idea.
Contributor guide
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Research direction
Start by locating the salmon processor's run_tximport_for_experiment() function and reviewing how it currently handles RNA-Seq experiments and organism associations. Consider the behavior for experiments with two or more organisms, then verify that multi-organism experiments can be processed without the current failures and that their samples are processed successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100