Not all samples found

[olgabot]

For PRJNA143627, only 106/149 samples are retrieved. Here is a notebook comparing the SRA explorer vs the NCBI run table output: https://github.com/czbiohub/kh-analysis/blob/olgabot/brawand2011-extract-coding/notebooks/410_compare_sra_explorer_to_ncbi_run_selector.ipynb

Here are the files: (had to add .txt so that GitHub wouldn't complain)
brawand2011_metadata.csv.txt
sample_metadata_handmade.csv.txt

[olgabot]

It doesn't seem like only the "First n" entries were found. It seems consistent and just reproduced it:

[ewels]

For PRJNA143627, only 106/149 samples are retrieved.

Yup, results are limited to ~100 samples. If you tell it to start at record 100, it finds another 42:

If you set the max records to 500, it finds all 149:

TSV of full metadata: sra_explorer_metadata.tsv.txt

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It doesn't seem like only the "First n" entries were found.

You mean it found 107 instead of 100? That will be because one or two entries will have multiple SRR entities. They don't always match up 1:1.

Does this solve your problem, or am I missing something here?

[olgabot]

ohh okay. I was confused because 107 > 100 so it looked to me that it found ore than the limit of results, so I thought it was done! Maybe something to clear up in the documentation

[ewels]

PRs welcome! 😁 I'm not totally clear on the what was confusing so would actually really appreciate any suggestions for what could be improved 👍