AlexsLemonade / AlexsLemonade/refinebio

Support RNA-Seq experiments with more than one organism

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Python
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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

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