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almost no genes detected #133

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wangjiawen2013 opened this issue Feb 1, 2024 · 0 comments
Open

almost no genes detected #133

wangjiawen2013 opened this issue Feb 1, 2024 · 0 comments

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@wangjiawen2013
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wangjiawen2013 commented Feb 1, 2024

Hi,
I followed the alevin-fry tutorial to process my customized feature-barcoding data, there are 19000 feature barcodes with 40 bp length each, the result are very weird, the gene expression quantified by alevin-fry is only 4% of that detected by umi-tools:

here is the statistics from featureDump.txt
image

CB CorrectedReads MappedReads DeduplicatedReads MappingRate DedupRate MeanByMax NumGenesExpressed NumGenesOverMean
ATAAGTGG 2234215 2188286 40832 0.9794429 0.018659353 0.0018865345 5228 914

The deduplicated reads is only 40832, but it's 1003469 when using umi-tools. What's the reason ?

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