<p>If processing a huge table with lots of &quot;false positives&quot; is OK, then you could enter your search term, from top right choose &quot;Send to&quot; &gt; &quot;File&quot; Format: &quot;RunInfo&quot;.</p>

CC BY-SA 4.0
2021-02-26T13:41:27.953Z
2021-02-26T13:41:27.953Z
Michael
<h3>The Question</h3>
<p>I want to find high coverage SRA entries, e.g., above 100x.<br/></p>
<p>I guess the best way is to use <a href="https://www.ncbi.nlm.nih.gov/sra" rel="noreferrer">https://www.ncbi.nlm.nih.gov/sra</a> with an appropriate search term. I don't mind if the search results contain some &quot;false-positives&quot;. (I.e., if some of the found entries have coverage above 80x, while I aimed for 100x, that's fine.)
I want to avoid using Entrez.esummary on a very large number of SRA entries (e.g., through Biopython), as it would be significantly slower (if I understand correctly).</p>
<p>How can I do that?</p>
<hr />
<h3>My Attempt</h3>
<p>I tried using the <code>Mbases</code> field.<br/>Assuming the reference genome is at most 100kbp (e.g., in case I am interested in viruses), I thought a good approximation would be to search for SRA entries with more than 100*100k bases, i.e., at least 10M bases.
According to <a href="https://www.ncbi.nlm.nih.gov/books/NBK3837/" rel="noreferrer">https://www.ncbi.nlm.nih.gov/books/NBK3837/</a>, I thought I could use the search term <code>10:9999999[Mbases]</code>, but disappointingly, this didn't work. Just to make sure my syntax is right, I verified that <code>100:101[ReadLength]</code> works. So it seems that <code>Mbases</code> doesn't support the range syntax.</p>

<ngs><database><public-databases><phylogenetics>
How to search for high coverage SRA entries
# How to search for high coverage SRA entries

(Asked by: username_0 on 2020-12-26)

### The Question

I want to find high coverage SRA entries, e.g., above 100x.

I guess the best way is to use <https://www.ncbi.nlm.nih.gov/sra> with an appropriate search term. I don't mind if the search results contain some "false-positives". (I.e., if some of the found entries have coverage above 80x, while I aimed for 100x, that's fine.)
I want to avoid using Entrez.esummary on a very large number of SRA entries (e.g., through Biopython), as it would be significantly slower (if I understand correctly).

How can I do that?

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### My Attempt

I tried using the `Mbases` field.  
Assuming the reference genome is at most 100kbp (e.g., in case I am interested in viruses), I thought a good approximation would be to search for SRA entries with more than 100\*100k bases, i.e., at least 10M bases.
According to <https://www.ncbi.nlm.nih.gov/books/NBK3837/>, I thought I could use the search term `10:9999999[Mbases]`, but disappointingly, this didn't work. Just to make sure my syntax is right, I verified that `100:101[ReadLength]` works. So it seems that `Mbases` doesn't support the range syntax.

**Tags:** ngs, database, public-databases, phylogenetics

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## 1 answers

### Answer by username_1 on 2021-02-26. Score: 1

If processing a huge table with lots of "false positives" is OK, then you could enter your search term, from top right choose "Send to" > "File" Format: "RunInfo".


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