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mritchielab / restrander

MIT License
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issues with pychopper and direct cDNA #4

Open sparthib opened 5 months ago

sparthib commented 5 months ago

Hi there,

On the ONT community website, there is a warning against using pychopper for direct cDNA data using the LSK114 kit claiming that "Pychopper currently miss-classsifies The reads generated with Direct cDNA Sequencing are not being classified correctly in the analysis workflow, leading to ≥80% data loss of full-read transcripts"

I was wondering if you are more familiar with this issue and have an idea of restrander's performance with direct cDNA protocols from ONT.

Thanks, Sowmya

jakob-schuster commented 5 months ago

Hi Sowmya,

As far as I know, Restrander should have no issue with direct cDNA data using the LSK114 kit. I've just added a config file for it using the primers from this document. If you download the latest version of Restrander, you can try it out using ./restrander input.fq.gz output.fq.gz config/DCS-LSK114.json.

We don't have any local DCS LSK114 data to test it on - if you do try it out, please let me know if it works, or if there are any issues!

Thanks Jakob

sparthib commented 5 months ago

Thanks Jakob! Will test this out.

Sowmya