Update alevin.rst

doc/source/alevin.rst

@@ -190,6 +190,9 @@ A typical run of alevin will generate 4 files:
 * *quants\_mat\_rows.txt* -- Row Index (CB-ids) of the matrix.
 * *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.
+
 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.
 
 Alevin can also dump the count-matrix in a human readable -- matrix-market-exchange (_mtx_) format, if given flag `--dumpMtx` which generates a new output file called `quants_mat.mtx`.