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Smart-Seq2 kallisto analysis pipeline #235
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Hi zolotarovgl:
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SMART-seq2 does not have UMIs so while one could possibly wrangle the pseudoalignments into BUS format the resulting BUS files wouldn't have useful information beyond what would be produced by running kallisto pseudo. SMART-seq3 does include UMIs and we do plan to provide a kallisto | bustools workflow for that. |
Hi @lakigigar ,
In this case maybe we can use the read two as 0,0,8 and 0,8,16 to specify the cell barcode and umi? |
We have used kallisto to process SmartSeq2 data for our recent manuscript Isoform cell type specificity in the mouse primary motor cortex You can find the relevant code here: https://github.com/pachterlab/BYVSTZP_2020 |
Dear kallisto team, I have two questions regarding the workflow with kallisto pseudo.
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Dear
kallisto
team,I have Smart-Seq2 data which I would like to analyse in kallisto:bustools framework even though it lacks UMIs.
I tried to search for related issues but didn't find any.
Is there any pipeline you can recommend?
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