BUG: Cannot handle multiple runs
Pipeline cannot handle experiments (samples) with multiple runs... for example:
| sample_id | sra_number |
|---|---|
| Sample1 | SRX172938 |
fails because SRX172938 has 4 runs:
| Run | # of Spots | # of Bases | Size | Published |
|---|---|---|---|---|
| SRR531404 | 5,261,058 | 189.4M | 93.6Mb | 2012-09-11 |
| SRR531405 | 6,870,169 | 247.3M | 204.4Mb | 2012-09-11 |
| SRR531406 | 7,941,818 | 285.9M | 236.8Mb | 2012-09-11 |
| SRR531407 | 31,599,710 | 1G | 605.1Mb | 2012-09-11 |
Advice
one or a combination of the following:
- make a note in instructions pointing out that the pipeline fails with samples with multiple sequencing runs and that users need to split those SRX's into separate SRR downloads
- don't accept any SRX's
- in check design, make sure that samples don't contain multiple runs and error if it does
- in check design, make sure that samples don't contain multiple runs and automatically split them
- if split then, consider concatenating SRR's after if submitted as 1 SRX