A multi-experiment resource of analysis-ready RNA-seq gene count datasets


ReCount is an online resource consisting of RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, we combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available here. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

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  • VLDS poster, 6/11 (coming soon)



The table on the previous page includes count tables and ExpressionSets created by running Myrna with the truncate=35 option, while the table on this page provides the count tables and ExpressionSets created by running Myrna without the truncation option. Datasets not included on this page were not affected by the truncation (i.e., their reads were no more than 35bp). The -v 3 Bowtie option (rather than -v 2 ) was used for the studies containing reads of length 50bp or longer to allow for 3 mismatches rather than only 2 in the alignment step.

Datasets, without truncation

Study PMID Species Number of biological replicates Read Length(s), bp Number of uniquely aligned reads ExpressionSet Count table
bodymap not published, but publicly available here human 19 50, 75, 100 1,732,952,136 link link
cheung 20856902 human 41 50 761,310,848 link link
montgomery 20220756 human 60 36 *881,304,874 link link
pickrell 20220758 human 69 35, 46 *881,304,874 link link
wang 18978772 human 22 32, 36 222,319,658 link link
trapnell 20436464 mouse 4 76 64,075,691 link link
yang 20363980 mouse 1 36 27,647,780 link link
bottomly 21455293 mouse 21 70, 76 287,321,756 link link
hammer 20452967 rat 8 50 144,944,741 link link
modencodeworm 19181841 worm 46 36, 76 1,253,144,777 link link
modencodefly 21179090 fly 147 (technical)**
30 (biological)
75, 76 1,756,719,388 link link
*Montgomery and Pickrell read counts are for both datasets combined.
**The modENCODE fly study contained 147 replicates and 30 developmental stages. Replicates within a developmental stage were technical and may be pooled during data analysis if desired.

Code used for this table

Commands passed to Myrna
R code used to create ExpressionSets (requires Bioconductor and additional files)