Deduplication of umi from my celseqdata

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2.7 years ago

Parichitran • 0

Greetings, I have a CEL-seq data incorpatated with umi.The following are the details of my reads

READ-1 =8bp(cell barcode)+5bp(umi)
READ-2= (47bp)

I want to deduplicate the umi in my data.I am here attatching my Both read files header Click here for READ files header

SinglecellRNA umi cellseq cellseq2 barcode • 920 views

ADD COMMENT • link 2.7 years ago by Parichitran • 0

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Have you checked umi-tools (LINK)?

ADD REPLY • link 2.7 years ago by GenoMax 147k

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Yeah Actually I am trying with umi_tools only.But the total number of reads I am getting after deduplication by umi_tools is less compared to the read counts generated in the already processed research work. I also raised my issue with the tool developer itself.Still we couldnt reach any conclusion on my dateset.I am here attaching the link of the issue, it may give give u and idea of my problem https://github.com/CGATOxford/UMI-tools/issues/518

ADD REPLY • link 2.7 years ago by Parichitran • 0

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Alevin has a CEL-seq mode which takes care of mapping and UMI deduplication. https://salmon.readthedocs.io/en/latest/alevin.html

ADD REPLY • link 2.7 years ago by ATpoint 85k

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