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bvaldebenitom / SoloTE

GNU General Public License v3.0
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Probe-based scRNA sequencing #51

Closed blaverty closed 2 months ago

blaverty commented 3 months ago

Hi! Thanks so much for your tool!

I see in your paper the 3 datasets you applied SoloTE to used 3' scRNA sequencing or bulk RNA sequencing. Can this tool be applied to scRNA seq using the Chromium platform with probe-based sequencing?

bvaldebenitom commented 3 months ago

Hi @blaverty !

With "probe-based" sequencing are you referring to the 10X "Chromium Single Cell Gene Expression Flex" protocol? If so, I can take a look. In theory, if the BAM file is generated with the CB and UB tags, SoloTE should work.

I will run some tests, and let you know.

blaverty commented 3 months ago

Yes that is what I'm referring to. Thank you for checking, I appreciate it!

bvaldebenitom commented 2 months ago

Hi @blaverty !

I ran some tests on data available at the 10X Genomics, and SoloTE will work. However, since it is probe-based, it targets mainly genes.

You can try running it with the --dual flag, as it will allow counts from gene to also be used in TE expression. However, I only noticed that I got 0.2% of TE expression without it, and increased it to 0.3% when using the flag.

github-actions[bot] commented 2 months ago

This issue is stale because it has been open for 10 days with no activity.

github-actions[bot] commented 2 months ago

This issue was closed because it has been inactive for 14 days since being marked as stale.