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Update alevin.rst
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k3yavi committed May 8, 2021
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Expand Up @@ -191,8 +191,7 @@ A typical run of alevin will generate 4 files:
* *quants\_tier\_mat.gz* -- Tier categorization of the matrix.

.. note:: Working with R packages

Alevin generates multiple metadata files like the hash codes of the reference transcriptome and it's crucial for working with downstream R package like `_tximeta <https://bioconductor.org/packages/release/bioc/html/tximeta.html>`. Hence along with the above files, it's advisable to keep the complete output folder generated by alevin.
Alevin generates multiple metadata files like the hash codes of the reference transcriptome and it's crucial for working with downstream R package like `tximeta <https://bioconductor.org/packages/release/bioc/html/tximeta.html>`_ . Hence along with the above files, it's advisable to keep the complete output folder generated by alevin.

Along with the Cell-v-Gene count matrix, alevin dumps a 3-fold categorization of each estimated count value of a gene(each cell disjointly) in the form of tiers. Tier 1 is the set of genes where all the reads are uniquely mapping. Tier 2 is genes that have ambiguously mapping reads, but connected to unique read evidence as well, that can be used by the EM to resolve the multimapping reads. Tier 3 is the genes that have no unique evidence and the read counts are, therefore, distributed between these genes according to an uninformative prior.

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