Can ALLSorts be used with long-read data?

[mariasolruiz]

Hello,
I have leukemia samples sequenced by cDNA-ONT, I would like to know if it is possible to run ALLsorts to predict ALL subtypte. Have you ever tried it?

Thank you,

Maria Sol

[aliciaoshlack]

Hi Maria, We have thought about this but haven't tried it. In theory you can use your ONT data to get gene level counts and then just run the ALLSorts classifier on the count level data. We have tried this style of approach on other types of data such as single-cell with some success so my guess is that it will work OK especially for subtypes such as Ph-like. However the data and counts are different to short read data so I can't guarantee the same sensitivity. Cheers, Alicia

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[mariasolruiz]

Thank you Alicia,

we will do some tests and let you know.

Best,

Maria Sol