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Kit used for cDNA synthesis #83

Closed AlvaroBernardino closed 3 months ago

AlvaroBernardino commented 7 months ago

Ask away!

Greetings! We're about to run a small batch of transcriptomes using SQK-NBD114.24 Native barcoding kit. While studying the workflow today I noticed that there isn't an option for this in "Kit used for cDNA synthesis". Should I select SQK-LSK114? Would it be compatible?

sarahjeeeze commented 6 months ago

NBD114 is not a supported transcriptome kit. The resulting reads will not be able to be stranded, which is needed to correctly identify genes and transcripts. The existing adapter sequences in Pychopper won’t be any use either. You to use try --direct_rna option to skip the Pychopper step and so not have reads thrown away when the adapters can’t be found

AlvaroBernardino commented 6 months ago

Hi, Sarah, thanks for your help! So if I understand it correctly, I could run DE analysis with the kit I have if I skip the pychopper step? Would that affect the quality of my data in any way?

sarahjeeeze commented 6 months ago

It's hard to say as we have not tested it but I would suspect you may get less transcripts overall as some may not align as well with but the quality of the ones it does find should be fine.

AlvaroBernardino commented 6 months ago

Thanks for your help, Sarah We'll run a test on a used flowcell before doing the real thing and I'll be back to report the results for future reference.

sarahjeeeze commented 6 months ago

A report back would be great thanks